For me it's the Megaman Battle Networks.
Albeit more childish compared to how somewhat dark X was, I still found it fun when I was playing it in my teens. Most side quests, and even one point in BN3, give you items that you can use, or set amounts of money that you have to deliver to someone else. But if you give into temptation, or somehow lose the item they give you (most of the time they are battle chips that you can trade in for others), you have to go out and get another one to progress the side quests.
The combat isn't bad. It's good, but not amazing until you get into the later games. It's a breath of fresh air from the side scrollers IMO.
I do like how the bosses actually have story's connected to them, rather than just heading into a giant robot fortress and killing a baddy without a reason, other than it's evil. The story's actually a bit dark, as the bad's intend to kill or hurt the world (they cause ovens to set on fire, try to suffocate people in a convention center, poison a town's water supply, (I think they caused a landslide on a IRL railway from the internet. Don't ask me how that works), etc).
Unfortunately, Starforce didn't live up to Battle Network
Whats your favourite underated/hated game/game series?