Yes you are right.
RPS Ken Levine interview on 1999 mode part 1http://www.rockpapershotgun.com/2012/01/23/youre-going-to-suffer-levine-on-1999-mode/#comment-page-3
Levines words are very worrying-
then this guy says “I’ve got a bone to pick with you, Levine!” He’s giving me a hard time, he says “the problem was none of the decisions I made had any permanence to them. I didn’t have to commit to any decisions.” And I was like “oh!” The clouds parted for me. Except for the Little Sisters, there’s no permanence in your choices. It hadn’t really crystallised for me before, the difference between games we had made before, like System Shock 2, and BioShock.
choice and consequence is not the only difference.....
This will only be Bioshock with slightly more engaging gameplay, not another Sshock 2. there is many factors why Sshock 2 is superior, not just choice and consequence- deeper immersion design, deeper survival horror design, having to use your brain in approach to enemy encounters, inventory, environment and character customization....... more gameplay options like mantling, 2ndary fire mode, swimming, 40 psi powers opposed to 10 or so plasmids, the RPG systems based on travellers methodology (I don't know alot about this "methodology" but it sure works well for SS2, balancing issues aside) and interaction, There is tons more factors. I don't see Shock 2 being the superior game just as an opinion, but as a superior design and craftsmanship overall. you can even pick up plant pots for [censored] sake, just to create a more believable and immersive experience. well and it can clog up your inventory if you do not throw it away, but its up to you, the gamer, to do so and not be an idiot.
Thats not to say Bioshock is not to be considered a masterpiece too, but its design has less depth in many ways, and less is certainly not always more.
1999 mode is better than nothing for sure but if the game was originally designed with these kind of systems in mind instead of building it to accommodate the systems already in place only then
maybe will infinite be worthy of the LGS legacy. But hey i wouldn't really expect games to evolve better than Sshock 2 and deus ex, those two are are good enough, but it is possible. the legacy got svcked into the mainstream. that's business i know, but i think we are ready for it to return, fallout new vegas is the definitive example of success and depth.