Mass Effect series:
They killed the deep exploration of the first game because too many people complained and replaced it with dull collecting that only makes sense if you want everything to go perfectly in time for the next installment. Which means I probably won't go through it a second time.
Bioshock series:
Look, we get it. Rapture is awesome. But we don't have to focus on eye-popping visual marvels. That's what the first game was about: getting us familiar with the world. If there is a Bioshock 3, focus on how the events of the first two tie into the ongoing history and characters instead of focusing on the brilliant beauty that Andrew Ryan created.
Grand Theft Auto series:
Try out a new city. One you haven't experimented with and one that doesn't immediately pop into sandbox simulation stereotypes (i.e. New York City). Maybe try out a sightseeing GTA game wherein your character is sent to three different places across the globe to track down an enemy. Maybe start in Russia, go to France, then end it on top of a Hawaiian volcano. Yes, it's a stretch, but it beats going between the three most popular US metropolitan areas for each installment.
Battlefield: Bad Company series:
This is probably my most reluctant response because I find the multiplayer quite enjoyable. Nevertheless, the single player needs some fixing. If you're up against a series known for its giant memorable campaign setpieces, don't use a convuluted plot about a superweapon and a deadly soldier to give an excuse to go through numerous forgettable firefights before a surprisingly awesome final mission that gives the impression that the rest of the game could have been as good as that. Yes, I found some of the dialogue to be humorous. Yes, I actually quite liked the pilot character because he seemed like the one original character in that type of modern war setting. But the mission structure needs an overhaul.
EDIT: Also...
Assassin's Creed series:
The first game was left on too much of a cliffhanger while the second used a mystery to make things a bit more engaging. For the third game, explain what most things mean, leave some things to be debated, and end with a great, striking piece of imagery instead of leaving us with a "What does it mean?" ending.