Soviet Heavy said:
Does anyone else feel like Side Quests need a bit of an overhaul?
Not really, there's a simple fix for this problem. Actually two.
If the main quest is played up as an urgent zomg gotta do it right now thing, let the player continue playing afterward.
Or!
Hold off on making the main quest seem urgent zomg gotta do it right now galaxy needs saving until the player proceeds far enough down it that it's reasonably safe to assume they intend to complete it soon.
Fallout 3 went the latter route. At almost any point along the main quest, you could divert without really destroying the story.
The "finding Dad" part could quite reasonably take a while. Don't worry though, he's somewhere safe.
The "cleaning out the memorial and restarting Project Purity" part is fairly weak though. I imagine they'd eventually get tired of waiting on you, and either get Brotherhood help or take some Rivet City security guards to clean it out. There's a natural resting point right at the end of that part though.
The "Getting the GECK" part could easily take a while. It didn't really
feel that urgent to me anyway. And then getting back afterward--well hell, no rush there either. Plenty of time for side quests.
Only once you start "Take It Back!" are you really locked in story-wise, where it doesn't make sense for your character to up and leave.
Mass Effect could be said to take the second route, depending on where you were in the main plot when you diverted off of the main quest. It starts off as a sort of mystery, and it doesn't break the story too much to go off on a wild goose chase and accomplish some side missions along the way.
Contrast that with New Vegas, where they try to make it seem like battle is imminent at Hoover Dam, and you're always one step behind Benny (so it would be logical to hustle to the next stop in hopes of catching up).