-- Steelport being even blander than it was in SR3. I didn't really notice it when playing through the story because of the superpowers. However, once I beat the story, turned on a SR3-native time of day skybox, and actually drove around the city, I was really disappointed to see it was pretty much the same, but lacking even more personality. They removed all the various ships that were docked or wrecked around the coastline, multiple buildings were destroyed to put those towers up, cribs and strongholds were no longer a thing, and they didn't even try to make up for this by allowing us to explore the various nightmare simulations afterwards. I can't remember where I read/heard this, but Stilwater was a great city because every mission took place in the city itself and it felt like they designed the city around the missions. Meanwhile, how many missions in SR3 and especially SR4 take place in Steelport vs. an area that's only available in that mission (a different simulation, a plane, skydiving, etc.)? I always held the opinion that SR3's missions were more interesting than the city itself, and that goes double for SR4.
-- The superpowers as a whole make weapons and vehicles mostly useless, but worse than that, super sprinting and jumping make active superpowers useless. Why waste time taking aim and shooting something when you can just sprint in their general direction, hammer the attack button to do a beatdown, then super jump to a nearby rooftop to catch your breath when things get hairy? I used the cheat to disable super movement after I collected all the clusters, and based on my time playing like that, I honestly feel like super movement shouldn't have been introduced in the game until over halfway into the story. That way, you get plenty of weapon and vehicle use outside of story missions before everything gets broken. Or at the very least they should've nerfed the initial speed and jump height and locked the upgrades away until a higher level. I understand why they did this though: to get all the awesome stuff to the average player quicker. Same reason why the Dubstep Gun was given as an early game optional reward despite it also being a late game story mission reward.
-- Forced upgrades. Now I understand that Volition had technical issues in not being able to toggle upgrades (hence why dual-wielding is still permanent), but what I really hate is that some upgrades that are rewards for side quests are automatically activated when you earn them. Why couldn't they have just been unlocked, allowing you to then purchase them? I'm having way less fun simply fucking around with telekinesis because one of the upgrades drastically increases the damage of a thrown object, which causes most cars to instantly explode rather than horrifically crush whatever NPC I'm throwing it at. This also goes for No Ragdolling from Vehicles, which prevents me from running into a car and ragdolling myself on purpose (yeah, I could just go into Insurance Fraud, but I like just goofing off every now and then!)