With the exception of the Dragon Quest installments they worked on, I've never found Level 5's RPGs to be particularly enjoyable. I'm not sure if it's the weak writing, boring combat systems, or higher emphasis on synthesis/alchemy, but I just can't get into them.
Those would be some of my general pet peeves with RPGs, as well.
Finally! A kindred spirit.
Count me in there as well. I don't think Level-5 has done much that's very impressive, and when they do they're good to milk it (I def think Layton is a great series). I think it'd be great to see a modern take on Dark Cloud, DC2 was pretty good and had a ton of great ideas.
Anyways. Some of mine.
= Why the punishment? If I want to or NEED to run from battle, please, just let it fucking happen (I only do it for two important reasons; (1) Because I'm about to die and don't want to lose my progress or (2) Because of my next point...)
= Random battles against foes way, way, way, way too fucking weak. I love that Xenoblade "gets" that you're going to kill a monster because you're 40 levels higher than it... the creature smells the blood on your blade and stays the fuck away and saves you the needless time wasting.
= Whatever the developers think a good walking/running speed for your character needs to automatically be cranked up AT LEAST 15%. I saw a video where they did that for FF14 and it was beautiful.
= Redundant menus. Skyward Sword, what the fuck. Pokemon, yeah I know I levelled up, and I know that a skill will be lost forever if I ditch it, you don't have to ask me if SUPER-SURE that I want to get rid of it because I've been told of this risk the LAST HUNDRED TIME YOU ASKED. >:(
= Lack of puzzles. Have you noticed how shitty dungeons have been the previous gen compared to the RPGs on the GC and PS2 and before then? Literally, there's like dick-all to do in dungeons these days.