The way I see the whole linear/non-linear design debate is in the question of is there a world to explore or is it all just fancy decorum for the hallway you're being railroaded through. The major factors involve matters of backtracking versus points of no return, permanently missable content, the number of available options at any given point, world scope, and side content.
In the matter of the RPG in particular, the objective of non-linearity is silly since the entire point to the genre is the effort of taking a character (blank or otherwise) and progressing them through a series of challenges until they reach the pinnacle of their abilities. Most games give you somebody new and fresh to take and to grow into what you want or need it to be to accomplish the goals set out for you. And this process is usually on a one way street (once you get stronger you can't get weaker because that pushes you further from completing your goal). And because your character can only grow in one direction so too does the game itself progress in one direction to push you closer towards the set goal.
The question then becomes a matter of how the game goes about this.
The most linear version of this lay in typical dungeon crawlers and side-scrollers. Side-scrollers will only let you move to the right so that you can push forward on a particular path through some kinda of obstacle course whereas dungeon crawlers only really let you push downward. Both can have pit stops in between stages but they otherwise complete ignore everything else in favor your single-minded charge towards the goal of the game. The problem I have with this design type is that if I get bored with this single-minded endeavor then my only option is to walk away. In fact, the only way I'd care for the dungeon crawler type of game (side-scrollers can be challenging enough to be worth the challenge on their own) is if the resource that needs to be managed is female clothing, all other potential motivations are meaningless to me due to the lack of context and the near meaninglessness of other resources due to abstraction (i.e. MP).
Your standard JRPG tends to fall into this process as well, especially games like the Grandia series where pretty much everything else is disregarded aside from pushing towards the goal except for the little pit stops between dungeons. The problem I have with this design lies in the fact that in a RPG where the idea of gradually grow stronger is lost on the fact that the challenge curves with you. Where new options are made obsolete as soon as you get them (status effect spells and such), newer and flashier kill sticks simply replace old ones, and the only real sense in progression comes either from watching the arbitrary numbers rise (both in regards to what you do in addition to what the enemy does) or seeing old bosses become random encounters.
Route splits are kind of a weird thing to place since it relies entirely on permanently missable content and Chrono Cross falls squarely into this one with its routes that determine which character(s) you recruit during your run as well as most SRPGs. Depending on how it's handled you could have multiple possibilities available to play through with multiple end goals in a CYOA (Choose Your Own Adventure) way at best or merely a cosmetic way to pad content by sticking a brief divergence in the plot that only those OCD enough will want to see (made even better by weighing a clearly inferior choice versus a clearly superior choice) with numerous possibilities in between.
Some games like the earlier FF titles (up till VII) and the later Zelda titles (like MC) among others are games I actually like despite the linearity. This is mostly due to the fact that you don't often run aground of points of no return (a couple of dungeons in the FF games) in addition to the fact that there is a world to actually wander around in once you've gained the means. Incidentally I find Radiant Historia to fall into this level due to the fact that while the plot is both massively on-rails and restrictive as all get out it almost never crosses any point of no return (aside from the prologue but there's nothing there aside from the events of the prologue but w/e). You can always return to any point that you've previously visited and with it any region, any missed treasure, and any events therein.
Then I believe you start getting into the sequence breaking stuff here with things like the earlier Zeldas and the various Metroidvaina wannabes where you have a set sequence of events but there exists the option of saying nuts to that, either intended or not, and breaking the order. However in this you still have to do everything the game wants you to do and optional content is either sparse or at the end. It's alright depending on how well it's handled but I dare not try to list all the examples.
And then I believe we start to get into side quest line stuffs that tend to overshadow main plot line stuffs with games like Majora's Mask and Deadly Premonition. I tend to really enjoy games where the main objectives are there and all but the real meat of the game is off the beaten path like these. Powering up is mostly optional but recommended to do a bit of at least. Of course my one disappointment with them is that they get too easy when you go for everything.
And I feel that this point of the spectrum is where many WRPGs and many Square/crappy Squeenix games fall where the main plot is but one of many quest lines. The big difference between the level above and this one is that these games present all quest lines and not just side quest lines in rather compact segments, usually started by a quest giver of whatever variety. I'm kinda not that big on these types due to the lack of gravity on the main objective, especially in cases like FFTA where over 90% of the content is useless filler who's sole purpose is for grinding on.
And finally I believe we get an almost pure non-linear type of game where there's no real overarching plot at all. The ending stands on its own whereas the rest of the game is at best dropping the tools you'll need for the endgame while grinding you up and every step you take means that the enemies get stronger and that you need to be careful not to waste whatever constitutes as a step, or that neither parties really get any stronger at all. I want to say that LoM falls into this but it doesn't really since the side plots are substantive enough and the method of making enemies grow with you was pretty ineffective at best. Unfortunately the best example would be the Megaman series where you only need a few upgrades at best coming either entirely or almost entirely from bosses with whatever Skull Fortress being the actual wrap up.
But this is just how I tend to order things in regards to linearity/non-linearity.