Just to say, one of the things I really loved about Saints Row 2 was how you could choose to go after all 3 gangs in a non-linear fashion, each one having it's own storyline. And this was eventually topped off with you up against the big bad itself (Ultor). You really got the feeling that you were taking sh*t over, which is one thing that makes a great open-world crime game.
On the other hand, 3 felt linear as hell in comparison, and shorter as well (even with using side-activities as missions to pad out the length). Even if they all operated as one, I do feel each of the Syndicate gangs could have had their own mission arcs, and STAG serving as a final "big bad" rather than just being shoved into the story when it felt convenient enough. I guess Volition was attempting to do a more straightforward narrative, but it instead felt like a jumbled mess full of unnecessary plot points (the zombie uprising). Trying to justify it as being "wacky" and "over-the-top" doesn't excuse it either, imo.
I also wasn't a fan of the new characters, Zimos was just an irritating gimmick character and Angel was boring as f*ck. I wouldn't have minded if they hadn't killed off Gat so early, but alas they did for whatever reason. SR4 may have attempted to retcon this, but by then the damage was already done.
That's another thing that bugged me a bit about SR3. Removing the ability to pick who you go after first and in what order was what helped the game feel less linear, and it suited the game given how much could be customized (both with your character, and by SR2 being able to pick how your gang dresses and what cars they drive). Besides those side activities disguised as missions, the zombie thing also really felt like a pointless filler just to add more missions. I remember back when the game first came out and I did co-op with a friend, and even then we both agreed it was stupid and that the zombie craze felt like it had passed by that point already.
As it was found in this thread (where the information apparently comes from the official strategy guide), the story did in fact change multiple times during development. Looks like Gat was not going to be killed off, he would have had to have been rescued. And in another rewrite, depending on the choices you made at the end, either Shaundi would betray you and join STAG, or Gat would be revealed to have actually faked his death and joined the Syndicate.
No Steel Port. New city with some returning characters sure but it needs to feel fresh as well as fun even a little over the top.
Honestly, I wouldn't even mind a return to Stilwater (a much more updated Stilwater, obviously). That was a far better location than Steelport. Besides the fact that it was bigger and had more interiors, the city didn't look the same everywhere. You could actually tell what part of town you were in from the surroundings. Steelport's neighborhoods reused too many buildings and it all looked almost exactly the same. There was almost no variety in that city. Stilwater also felt more alive, NPCs actually did things, where as Steelport's pedestrians either walked around or stood in place most of the time. If they decide to create another new city, they really need to make sure that there's some variety. I get that they were trying to go for a Pittsburgh vibe with Steelport, but they really went overboard with trying to make everything look like sh*t.