I actually got rediculously close to completing Minish Cap 100%. Like, One Heartpiece away, I think, plus the Final boss (which I could never beat. That final form really is a pain in the butt. In fact, what Zeldas besides the Oracle games had a good final boss? Wind Waker?). Not even sure how I got that far...
- The Original had a decent one for the time (not as tough as the Gleeroks but Gannon could be tricky if you missed the Red Ring and have bad luck getting your hits to connect (or impossible if you fucked up and missed the Silver Arrows; don't do that)) but he's not really that tough on his own. Its the final dungeon itself that presents the real challenge (amusingly the First Quest's version is the more challenging due to being the largest dungeon in the game, to the point that it contains a one-way route that forces you to backtrack almost halfway through the dungeon if you make a wrong turn), as both filled with the toughest enemies (including those fucking Blue Wizrobes who hit reasonably hard, take a couple of hits with even the Magical Sword apiece, like to move around a bunch, and are occasionally prone to suicide rushing you while Link's attack is too limited and clumsy to deal with them effectively without getting injured in the process; unless you have the Swordbeams, then its just a matter of not losing them) plus minibosses all over the fucking place.
- Adventure of Link had a double whammy of the Thunderbird and the first Shadow Link which all but guaranteed the loss of a life due to the fact that you had to bleed over half your Magic dry to even fight the Thunderbird (thanks to having to cast Thunder to actually harm the bastard and at best, that spell guzzles half your total MP), let alone Shadow Link who's pretty much one of the most difficult foes in the entire series (after the requisite Thunder, you'll only have enough MP to cast one charge of Life or two charges of Shield). And all of this is at the end of the Great Palace which is only a grueling gantlet if you know where you are going (Internet help you if you don't).
- Link to the Past had probably the toughest Ganon fight in the series due to the sheer amount of damage he took and dealt (even through the Red Mail, you're getting pounded) and that several of his attacks have huge AoEs that like to punish you for getting too close (and you have to get close to actually harm him). Fortunately, he has no dungeon to wear you down before fighting him and you have an easy way out if things go south (or if you screw up and get knocked out; or if you somehow missed/forgot the Silver Arrows) which is a lot more than the previous games gave you.
- Link's Awakening has an interesting final boss since its mostly a walking reference to previous major Zelda bosses (and Moldorm) and the final form isn't a total cakewalk.... Unless you brought the Boomerang, in which case Nightmare folds faster than a cheap suit, and you might as well since actually navigating the maze to get to the final boss requires completing the Magnifying Glass sidequest which is literally one step removed from acquiring the blessed thing (and how much do you actually need the Shovel anyways; especially after getting the Level 2 Sword). And that's not even getting around to the DX Mails.
- Ocarina of Time's version of Ganon is a very cinematic fight, but not a very challenging one. Even his dungeon is both short and kind of a bore compared to what came before it, and even without the Defense Boost, N64 era Fairies pretty much make you immortal. Only the countdown timer can actually be threatening during the whole sequence.
- Majora's Mask's Majora can be fairly challenging if you aren't fully kitted out or at least rocking about 80% of the game's collectables including missing one or more of the major upgrades like the Gilded Sword or the Defense Boost since he hits fast and has massive AoEs on his attacks. But 100% upgraded and Majora ain't no threat and he's completely fucked if you brought the Fierce Deity mask (especially if combo'd with a Cheateu Romani or even a Green Potion or two; and you still have enough room for "FIVE" more Blue Potions/N64 era Fairies).
- The final bosses of the individual Oracle games themselves are actually fairly solid, especially Season's, but Ganon himself is pretty lame since he's too busy trying to be intimidating to actually be intimidating (and then you factor in one of the better rings....). Hell, even Twinrova puts up a better fight than him and that's mostly due to her gimmick and you not thinking to bring the Snowshoe Ring with you.
- The best things that can be said about Wind Waker's final battle is that your fight with Ganondorf is really stylish and actually develops a bit of, dare I say, 'challenge' near the end, which given how much of a total pushover the rest of the game had been up to that point is definitely a point in its favor. Another point is that the Ganondorf fight can be considered more of Puppet Ganon's final form rather than his own thing but Puppet Ganon isn't really that tough and Ganon's Tower, which you have to climb to get to these fights, is an exercise in sleepwalking (not only did you fight Phantom Ganon once before but due to having to fight him repeatedly, he's treated as little more than a gimmick; and he's all the challenge the 'dungeon' actually has beyond the final boss fight). That said, Elixir Soups and the Magical Armor exists in this game and the Fairies are still N64 era game breaking so in the end its still about as challenge as the rest of the game (i.e. baby mode).
- Four Swords' final boss Vatti is pretty much the same as every other boss in Four Swords. Boring as shit.
- Minish Cap's final boss was discussed before but bears repeating that its amazing at just how much of a difficulty spike Vatti presents compared to the rest of the game. Its probably due to the fact that Vatti doesn't really waste his time with crappy first/second forms and remains challenging throughout all of its change-ups. Its also probably due to the game not handing you an "I Win!" button or enough overpowered bullshit to completely trivialize the fight. That said, he's still no Shadow Link or LttP Ganon and 15+ Hearts + a Bottle or two should still suffice against him and his final dungeon can be backed out of easily enough (and is necessary to do so to actually 100% the game due to
all the arbitrary plot based gating the Mirror Shield being post game only
Figures being total dogshit).
- I've seen Four Swords Adventure's final boss in action twice now, and I still can't quite recall how challenging he is. Sure he's modeled after LttP's Ganon but given how generally non-threatening singleplayer mode is (due to the complete lack of multiplayer dickery), he can't be that hard.
- Twilight Princess's Ganon/dorf fight is only hard if you aren't getting the timing on the
Ganon-wrangling down. Otherwise, the Ganondorf fight is fairly atmospheric but the entire thing is a montage of "let's use every major game mechanic gimmick" that the series has grown to love lately. At least the Potions/Fairies finally got nerfed to accommodate for the fact that enemies do crap for damage to you.
- Phantom Hourglass does the same thing as TP with its "gotta use them all" game mechanic bullshit. Its just not as bad due to the game not having that many compared to the two surrounding it. Also its nice seeing Linebeck do something other than berate you for not being him/being his gofer (as amusing as that may be).
- Spirit Tracks has by far the worst final boss fight in the series since it again has the "do the gameplay mechanic gimmick shuffle" that the previous two games stoop to, except that the game is flush with gimmick mechanics. Especially since you've got like four separate bosses (the trains, the big evil train, the evil chancellor dude and the big bad himself), each with two or more forms, and several of which are just straight up ripping off non-Zelda games like Pac-Man and Galaga. That said, none of the fights are difficult. Just frustrating.
- Skyward Sword has a really interesting final boss sequence, especially if you count Ghirahim's portion since he gives you a chance to feel like a badass by having you mow down mooks to get to him, then smack he himself back down into the pit you just climbed down into. Then Demise is all about whether you get the Lightning Bolt gimmick or not. He's tough but doable without it (especially if you got the Hylian Shield beforehand), but he's still at least middle of the road with it. Really though, they're totally badass, they make you feel totally badass, and are really good just for that alone.
- And finally is A Link Between Worlds which tries to up the ante from LttP's Ganon fight but Yuga's attacks are easier to dodge/block/can be blocked and aren't quite as damaging and the fight itself isn't quite as long or involved as LttP's. I'd rate him closer to Demise with the Lightning Bolts level if you're fully kitted out, and about WW's Ganondorf hard without. Either way, the dungeon doesn't add much.
The tl;dr version is that challenge wise I'd go:
AoL > SS (without Lightning) >> aLttP >>>> MM (with <80% upgrades) > MC >>>>>>>>>>> SS (with Lightning)/ALBW > LoZ/LA (without Boomerang)/Seasons > Ages >>>> TP >>>>>>>>>>>> ST (due to bullshit) >> OoT/Oracles/PH >>> FS/FSA(?) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MM (with 100% upgrades)/LA(with Boomerang).
and coolness/badassery factor wise:
SS (metal as fuck) > WW (its really the cutscenes that make this) > AoL (Shadow Link) >>> OoT (music/dramatic lighting) >> aLttP (the capstone of a really solid game and the ending theme is amazing) >>>> LA (the boss is cool even if it goes down like a punk) >> MM (Fierce Deity on full tilt for total omnipotence)/Seasons (platforming on a goddamn dragon) >>>> LoZ (dat dungeon music)/Ages (switchhook central) >> TP (dat Ganon/dorf herding)MC (don't know why but Vatti's just not that cool)/MM (without the mask/proto Zant)/ Oracles (dat mindless Ganon)/ FSA (aLttP Ganon even if he is just kinda there)/ PH (Linebeck's a pretty cool dude in his own particular idiom) >>> FS (again Vatti just isn't that cool and he's got even less going for him this time) > * infinity > ST (Bedlam is just so fucking lame; oh wait, is that PH's boss? SO. FUCKING.... LAME!).