The biggest flaw in Battle Network 2 is the fact it's the forerunner of the worst staples of the series. Tedious "license" segments involving finding X thing and defeating a series of viruses, lot of conversation chasing with NPCs, cryptic or convoluted hints/mechanics, hunting for NPCs and items in obscure places, etc.
The first half of the game flows pretty well, but things slow down significantly once you hit the ice on the net.At that point, the game devolves into going back and forth between NPCs to get things important to progression to actually spawn in to places you've already been. Honestly once this bit is over, the remainder of the game goes by pretty quickly, not counting the post game.
There's also weird bottlenecks like requiring certain chips to get past certain points. My personal least favorite is having to pay 10K zenny to a navi in Undernet square for information. 10K isn't a lot, but it you've been spending it on HP Memory and PowerUps, you might have to stop and grind mystery data and random encounters for a bit.
Another problem common among this series are the shoddy translations, which sometimes makes hints for puzzles essentially moonspeak. Then you have moments where you press L to consult MegaMan or Lan for hints to story progression and get something stupid like "The net is in danger, we need to hurry!" Like yeah, no shit, but that tells me absolutely fuck all about WHERE or WHAT I need to be doing.
It's not as bad at BN1, but if you haven't played it through before, there are a couple spots that could leave you scratching your head wondering what exactly in the fuck you need to do.