"Would have, could have, should have" is always difficult, but I guess I can nominate:
-Command & Conquer: Tiberian Twilight
I'm more sympathetic to this game than most. From what I've gathered, it was stymied by originally going to be a different RTS game, and a short development time (in other words, EA screwed the pooch again). Thing is, I can see sparks of greatness in Tiberian Twilight's story. I could see its gameplay style working if it was fleshed out more. Instead, we get a story that tries, bless its heart, but just doesn't work that well, and gameplay that basically boils down to "out-spam the enemy." This is the game that effectively killed the Command & Conquer franchise, and boy is it a sad note to go out on.
-Golden Sun: Dark Dawn
Okay, I'll be honest - this is a good game. A game that doesn't capture the magic of its predecessors, and enters the "most disappointing games of all time" for me, but to be fair, when I'm forced to wait a decade for the third installment, and when I'm of the opinion that Golden Sun didn't need a third installment, I guess I'm going to be harsh. That said, Dark Dawn is the weakest installment in the series for me, and I guess if I were to change it, it would be in the following ways:
-Cut out Blados and Chalis. They're a repeat of the Saturos/Menardi and Karst/Agito duos, and they don't generate any intimidation. Anyone with a brain cell knows that Arcanus is Alex, so just cut out the middle men and focus on him.
-Cut out the Shadow Clan stuff. It's a cliche I've seen in a million Golden Sun fanfictions, of a supposed 5th/6th element. Dark Dawn excels over its predecessors in one key area, and that's its worldbuilding, soing a post-Golden Sun event world. So focus on the world rather than throwing in such an element.
-No cliffhanger. NO CLIFFHANGERS!
-Halo 3: ODST
I thought of nominating Halo 4, but I don't see how that game could be saved. ODST however, is fundementally flawed with its New Mombassa concept. It's tedious, it's annoying, it's poorly done stealth combined with poorly done open world. If Bungie had focused on actual missions and kept a linear game, I feel it would have been much better. Focus on having ODSTs be different from Spartan-IIs, focus on individual levels, and whoila. You have a good game, not "explore a city you can barely see because it's so dark."
-Perfect Dark Zero
Heard this was rushed - maybe, maybe not. But I could see this being much better than it ended up being if the gunplay was improved, and if it had a tone more in keeping with the original. At the least, it did spawn the Rucka novels, which executed the Perfect Dark setting much better in my mind.
-Sonic the Hedgehog (2006)
It's a given fact that this game was rushed to meet Sonic's 15th anniversary. I've played some of it, and while I don't think it's the worst thing ever, this game is fundementally flawed that people have spent hours dissecting. And what sucks is that looking at the game, I feel that this could have been a very solid entry. A return to the SA1 style of hubs + levels? Check. Three core characters with side characters with their different playstyles? Check. Enjoyable gameplay when it isn't glitching? Check. Make some adjustments to the story (e.g. cut out Elise, or make her a furry and/or capable character), and I could see this being a solid entry.
-Sonic Chronicles: The Dark Brotherhood
STH06 was flawed because of lack of development time. Sonic Chronicles is flawed because it's lazy. Like, really lazy. Like, "seriously BioWare, did you just copy-paste Archiverse material into the Segaverse seting, undermining the latter while not getting what worked in the former, coupled with some of the most generic music I've ever heard in a Sonic game? I could go on, but I refuse to put more effort into this than the developers did. Basically, Sonic Chronicles was ME3 before ME3 happened, coupled with just as atrocious an ending (yes BioWare, leave me with a cliffhanger that'll never be resolved, topped off with Sonic and Tails discussing the history of BioWare. Yep. That's what I wanted.)