I think the PC port gets too much grief. Yes, it was atrocious when it was released, and yes, the controls should have better utilized the mouse, but by the time it was properly patched it was quite an enjoyable and playable game. Call it lessons learned; if SR3 came out for PC as functional as the currently patched version of SR2, I'd be satisfied, and I'd certainly be a lot happier with that than not getting to play it on PC at all.
I'd like to see the expansion and renovation of houses and the Saints' HQ be functional as well as cosmetic. Someone else mentioned interactions with other gangs besides decimating them; it would be interesting to have impressing people with your digs being part of diplomacy and luring away rival gang lieutenants. I'd like to have a personal armory where I can respawn customized weapons. It would also be interesting to have more missions that involved defending your base, and somewhat more direct control over where your gang members concentrate and what kind of criminal endeavors they get up to. I don't think anyone would enjoy things getting "management-sim" level complicated, but it would be fun to be able to make people come help in areas where the enemy is thick, and perhaps add some flavor to see your gang members dealing drugs or boosting stereos from cars or running numbers rackets, for example.
In general, I'd love to see more action indoors. If there were more missions involving your HQ, you might end up discovering strategic advantages to where you put your entertainment center or ruing the day you decided to put that bar in the corner where it provided a sniper with cover. I enjoyed the missions involving places like the mall; navigating them was a bit of a pain at times, but they added a feeling of place to a genre where an awful lot of action mysteriously takes place outside, making all the skyscrapers in these sandbox cities feel like painted cardboard boxes.
And I know a lot of work must go into recording voices in SR, but I'd love to have a few more choices with regard to the plot. Must I always be a psychopath? I know gang leaders by definition don't tend to be warm and fuzzy, but I'd occasionally like options other than scorched earth campaigns against any and all opposition.