The amount of super-heavy weaponry later in the game is...odd. Maybe some sort of limitation on the number of such weapons a single randomized encounter can spawn could be implemented in GH2?
If a monster/weapon is supposed to be rare, no more than a couple should spawn under randomized circumstances. A nest of Hunter-Xs would have a Killer and everything under, but a simple monster nest might have a single Hunter class with plenty of 'lesser' firepower.
Maybe if we a set a 'threat range' for quest types, so you get more specific array of descriptions. Early on you get rats nests, but people quickly stop asking you to clean sewers once you get a reputation. They're more likely to ask you to go clean up a biomonster infestation. At very elite levels, they only offer you top-notch jobs. You can still find the others if you look for em, but you aren't gonna get a phone call asking you to deal with a local band of hoodlums unless they're the sort of hoodlums who burn cities to the ground with Dragon Ball Z-ish fireballs.
(This post in no way endorses the use of Dragon Ball Z-ish fireballs, or guys with funny hair screaming about things exceeding 9000.)
On top of that, a more diverse landscape, with more room for cover and evasive maneuvers would ease up on the relative danger of most encounters, or at least help the player control that danger more easily, so it isn't just his skill of 10 rolling against 6 skills of 8 and praying for a critical hit.
Most preferably, most missions could use maps where the player could prepare and act, rather than just spawning on a battlefield full of nasties. Instead of spawning in a field with the enemies east of you, you spawn near the edge of the map, with some message informing you that you're nearing the base/hideout/etc. Assuming it isn't an ambush scenario for the enemies, you should spawn in some sort of cover(if available), so the player can begin the mission with stealth in mind if he chooses. Giving the player more options on how he can carry out a battle would greatly aid players who prefer to work solo.
...I think I rambled most of that post, so blame any lack of coherence on my sleepiness.