If you mean Reincarnated Purgatorial Altar, I remember that one only being 10 (which is still twice the standard for important dungeons), and while there were a lot of data bugs, occasionally there would be normal enemies to burn infection on. The Quarantine bonus dungeon was that one that's 15 floors if I remember correctly. I made it through the final dungeon at sub-Max infection just fine, but with the bonus dungeon, I wouldn't attempt that unless at level 100. I might be wrong here, but I think if you're lower level compared to enemies, you might take more contamination in draining them. Additionally, if you were just exploring randomly, using those Fairy Orbs in dungeons (not merely fields) is great for helping to avoid unnecessary infection, as well as avoid really shit rooms (ones with two portals in them).
.hack in general its not for everyone though. I played the games recently and really enjoyed them, flawed though they might be. IMOQ is much more interesting on the story/character end than the actual gameplay, and I honestly had trouble seeing what, aside from the quirk of it being a VR MMO, would keep The World R:1 so popular if it actually existed. R:2 feels a bit more like an actual game world.
Wrong. The series was intended as a multimedia work from the start. The games are not an adaptation of the anime, nor are the anime adaptations of the games. They are interrelated though. Some of the manga and novels are adaptations of IMOQ and G.U. though.
G.U. is more fun on the actual gameplay end, since the Skill Trigger makes combat much less of an annoyance as you're not having to constantly open a menu, and Haseo becomes rather versatile as the series goes on. Data Bugs are gone, Virus Cores only show up in Vol.3 as optional items to increase your power, and Phase (and AIDA) battles handle as mixed hack-and-slash shoot-em-ups (not to mention you can actually see how close your enemy is to Protect Break). Data Seeds have similar plot usage as Virus Cores did in IMOQ (substitute Sign Hacking for Gate Hacking), and you'll get most of what you need through regular progression, though the game does like to throw the occasional "Not enough seeds, go clear X dungeon for a seed" at you, but only over a single, individual seed.
R:2 is still meant as an MMO though, so you're going to be visiting similar looking fields and dungeons repeatedly, though there is some attempt at changing things up via missions (usually "Kill the boss" or "open the chest on the Beast Temple") and quests every so often. For 100% completion, it's still annoying though. Some items needed for Ryu Book counts are only tradable in one game, and some of them are also subquest rewards for doing X Y number of times (there is some effort to not make things as tedious as they could be, by already starting count towards subquests at the start of the game, before a given quest even appears that would unlock the count). And if you miss wallpapers and BGM in one game, you can't get them in the next.
To be fair, I didn't exactly try for 100% completion of G.U. when I played after realizing what that entailed, but the only time I got seriously annoyed about forced-plot grinding was in Rebirth. There's a point where you need to fight the arena champion as part of an observation (and grudge match), and that entails grinding arena points to get into the tournament. "PVP" (in that you're still up against computers representing players) is an interesting diversion and a decent way to level up weapon skills, but until you reach the right number, it's just match after match after match until you hit the right amount of points to get in the tournament. Thankfully, CC2 seemed to realize that was a shit part, and the next two games grandfather you in with no further grind, albeit in exchange for your "Emperor" status.
In short, G.U.'s much better on the mechanical end (as well as audio and visual, if you ask me), but it's still repetitious at times, especially going for 100%. And depending on the player, Haseo starting off as an incredibly mean asshole of a person can be a real turn off (he does get better as the games go on). G.U. also has a timeskip between the introductory dungeon and the events at Hulle Granz Cathedral wherein .hack//Roots takes place, and helps develop Haseos relationships with Ovan, Shino, and Tabby, but the latter half of Roots (Haseo's coping with loss) is such an edgefest that it can be a turn-off as well. And for some baffling reason, the last four or five episodes have spoilers for volumes 1 and 2 of the games, making it lose some of its effectiveness when you can't watch those without spoiling yourself (something Sign handled much better in regards to IMOQ).