I don't want factions to be ignored they have a very awesome flavor unless it's like the goldside where if you make certain choices you flip alignment, but if I could pick two things to be reconsidered it would be removing all level limits from contacts and story missions.
I love the various little stories some of which can give great opportunity to real feel out the character concept you made, but having to do like 30 missions with exp turned off to not miss anything like badges or unlocking certain contacts would be a great QoL change I would really support. I don't mean for the content itself to change just those little limits that say "oh hey you're too competent for this job" to be turned off, because really who is going to stop while being beaten by some things and demand someone less qualified to save them instead?
Using Ouro to go back for certain things doesn't really have a good feel to it and some of the quests that recognize stuff done before don't seem to recognize it unless you've done the quest outside ouro which is an immersion breaker on top of another immersion breaker
The other would be doing away with paper missions and making the detective/broker thing for bank heists be unlocked by tips missions which are more fun to do while papers are purely a chore especially when you have to do 10 of them