Oh here we go.
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Rune factory Frontier:
The Runey System. Just...Remove it. Entirely. Or make it 100% optional.
Because managing a runey food chain was hugely annoying and distracting. Doubly so since your only tool for moving their populations around is a crappy little vacuum that has an AWFUL radius. The only way to lower the annoyance is to game the system and force an area to generate Grass runeys nonstop and then try to force areas into "prosperity" which simplifies the food chain greatly.
However, having areas in "prosperity" makes your crops grow faster. If you have 3 or more areas in prosperity, it becomes GAMEBREAKINGLY faster. Strawberries growing back literally every day kind of faster. And if you decide "you know what? No, I'm not dealing with this bullcrap game mechanic" and don't deal with the runeys...BAM, areas will go into "ruin" and if too many areas go dark, your crops will consistently literally die on the vine before they're ripe.
RFF was the perfect Harvest Moon type game. Great characters, the farming was fun, the Rune Factory Combat was nice and tight and responsive, It looked great, the whole thing was fantastic. And that one mechanic takes away a lot of time and energy from every day as you go "crap, I need to babysit the runeys".
Thank Goodness Rune Factory 4 did away with it. Although it doesn't quite feel as refined at RFF. That and aside from the dragon, and a rival you make during the story, none of the characters are all that interesting to me. :s
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Final Fantasy Chystal Chronicles The Crystal Bearers (The Wii game):
I have many gripes with this game. Not living up to potential, making traveling over long distances incredibly irritating, You're technically a wanted man but no one ever does anything about it (Aside from once in a while tackling you once in a while to make you drop money) even if you cause full-on mayhem, 80% of the map having the SAME shitty combat music, while the cooler Ice and Water Battle themes get like 2 areas where they play, etc...
But my biggest change is summed up in two words: More. POWERS.
Seriously, "lift and throw", with the occasional "enemy power" or specifically-timed throws is not enough to keep things interesting in the long run. Seriously, there's lots of neat stuff you can do with gravity! And it's not like the hero isn't using it creatively in cutscenes either!
I'd make it so that you have 2 slots for additional powers that you can swap out (operating on cooldowns or something), and make those tweakable by accessories.
New power ideas:
- After locking on to an enemy, you can press a button to rip debris up from the ground to use as projectiles on the locked-on enemy.
- The ability to yank enemies directly towards you, which could be followed by a gravity-boosted melee hit that turns enemies into team-rocket-style-stars if you kill one with it.
- A gravity-powered lunge at an enemy that knocks them back or stuns them for a second.
- Slamming Lifted enemies directly into the ground for extra damage.
- An AEO burst that sends enemies flying in your direct vicinity.
- A "jump" power that makes you briefly invulnerable (used as a dodge). Maybe have it turn into a melee kick if you land on something.
- The ability to crush enemies you've lifted.
But no. All we get are "lift and throw" and sometimes getting to "Steal" an enemy's attack while you're lifting them, and a few specifically timed things. *sigh* I mean, yeah, there are a lot of neat enemy interactions (goblins running up to dance around Self-destructing bombs, etc), but it still gets stale after a while.
And actually let me throw another thing up there. Once the Fast Travel Network Thingy has been unlocked, they should have made all the entry points show up on the map, and all of them should have been easy to spot. I mean...I only found about 4 of them. Most of them in one themed area. It makes travel way too annoying.
Oh, and could we have a way to prevent the "monster phase" of each area, if we want to continue messing around with the NPCs or looking for fast-travel nodes? Being forced to kill all the enemies, or just WAIT for 10 minutes for the portal to close is just not cool!
...*sigh* So much potential, yet it doesn't meet it at all. Not a bad game, but considering how great it could have been...
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Jak 2:
MORE CHECKPOINTS DAMMIT. AUGH. Or have stuff kill you a lot less rapidly!
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EDIT:
XenoBlade Chronicles:
Axe the whole "Heart" dungeon. Make it an optional one. Seriously, the game should have gone for the final dungeon RIGHT after the whole climax atop the mechonis. It dragged on for too long after that.
Oh, and have more leve-appropriate quests to do near the end. I was too low level to deal with the sudden difficulty spike at the end, and with no level-appropriate sidequests I had to grind on normal enemies for hours. That killed the whole momentum of the ending for me.

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That's all I can think of at the moment.