I acquired a copy of Phantasy Star II back in the late 90's, but didn't play through it until around 2010. The "less than stellar evaluations," you've read are fair, I wouldn't deny the validity of those perspectives. The story is only slightly more robust than Final Fantasy I for the NES, and the visuals seem pretty uninspired, even redundant. I wasn't impressed with the title when I first attempted it back in 98'. However, I dedicated myself to a playthrough in 2010 and was satisfied with the experience.
Certainly, Phantasy Star II is not for everyone. Even for a 80's/90's RPG, it's a real grinder with difficult random battles, and sprawling, featureless dungeons. Solving the game by ones own wit requires some attention to detail, fair resource management skills, and patience. As JRPG's go, this a tough one, but Phantasy Star's most redeeming quality is it's challenge. The scant extant story of Phantasy Star II eventually culminates in an interesting ending (nothing too mind-blowing, but amusing). The drama of an out of control AI initially designed to maintain a utopian world seems more relevant than typical JRPG fare. I also liked the setting, stretching across multiple planets in Phantasy Star II' s solar system.
I can definitely see why most wouldn't like the title, but I enjoyed the challenge and the setting. Also, I am one of those rare JRPG'ers that actually enjoys the grind. Though I prefer PSII be included on the mini Genesis, I'd be completely content with it's absence, so long as Phantasy Star IV were given a slot. Phantasy Star IV ratchets up everything good in PSII, and appears a much more refined piece of gaming art. PSIV is't quite as challenging, but seems superior in every other comparable category.