It had good voice acting...
Go listen to it again. The voice acting was my biggest knock against the original. Granted, it came in a day when very few games were fully-voiced, but it was bad....
Star Wars-prequel bad.
The rest of your points, I'll agree with after a fashion. The elements you listed worked well for the game because they played off of one another well. Players could choose their approach to a level, and different approaches would require different augmentations, skills, and equipment to be successful. You had to think ahead and ration out your money/skill points/aug slots to ensure that you were prepared for challenges as they arose. Specialization was rewarded, while attempting to flit about from one strategy to another was punished. It made for a cerebral experience and a satisfying one, when events went to plan. If the game had given you too many skill points, too much money, or too much flexibility with augmentation slots, then the whole game would have been a cakewalk, branching paths would have gone unnoticed, and the negative aspects of the game would have had more of a chance to stand out. Sure, it still would have had a leveling system and a currency system and multiple completion methods in each level and the setting, and all that would have come across as unnecessary bits tacked onto a middle-of-the-road, late-'90's shooter.
I just hope that Square-Enix understands all of that. They've been hitting the bulletted list of
Deus Ex features really hard, but if they don't get the gameplay elements to work together well and make an effort to both reward intelligent play and punish stupidity, then this is going to be just another brown, cover-based shooter.