As the resident "System Shock" fanboy, I nonetheless have to agree with Yahtzee on "SS2". The "repair" skill was absolutely useless, for example, whereas the "Maintainance" and "Hack" ones were essential. (I'd love to know if anybody has ever beaten SS2 on "Hard" or "Impossible" difficulty without putting at least three points into "Hack" early on.)
The "Exotic Weapons" skill was useless until the Operations level (almost halfway through the game) because you didn't get the crystal shard until that point. Heavy and Energy weapons were extremely specialised, whereas the "Standard" weapons included the two best weapons in the game, easily - the versatile pistol and the assault rifle - and also used the most plentiful ammunition. Standard weapons could be used on robots and annelids equally effectively (unlike any other weapon class). Yeah, it's fun one-shotting the Heart of the Many with a viral proliferator, but there's really no practical use for it before that point.
And I've only just recently got used to the psi-amp, after several playthroughs. It's a bit fiddly to use and you need to know what powers are useful and what are useless. The healing ones sound useful, for example, but there are so many health pick-ups throughout the game that they turn out to be something of a waste of cybernetic modules.
And stats? There's zero point in having anything more than three agility or endurance points, even on the very hard difficulty levels. Strength is essential for the heavy weapons, armour, melee, and just basically carrying stuff about. Psi is either essential or useless depending on your build. And Cyb is essential for a decent hacker build (which as has already been established is just about any useful build in the game.)
Incidentally, I bought a bunch of older games and am now playing through Deus Ex. Unfortunately the graphics really are seriously ugly, to the point that it's actually somewhat off-putting.
Half Life? Didn't have any problems with the boss fights myself, although the giant spider thing annoyed me. It seemed like a gigantic ammo drain.