Clearly it is different enough that it has ruffled some feathers and some customers feel that they have been "misled".
No, it's ruffled a single user's feathers who took the time to post. Pretty much every review of the game spoke highly of the system and poorly of the layout. There has been some issues taken that it is a skill-based game and that it lacks the D&D Attributes... there are plenty of threads here describing many of the differences between SSEH and C&C. In the end, SSEH is it's own game... it's not a D&D clone, it's not OGL... it uses the pure mechanic of the SIEGE Engine. Combat is a SIEGE check, Magic (really psionics, since it's sci-fi) is a SIEGE check... you roll your d20 and try to beat 12/18 depending on your Primes... instead of primes being tied to attributes they are tied to "Skill Bundles" which is a way of thinking of classes in SSEH... your class is your skill bundle... if you have the Combat Skill Bundle then you are some kind of fighter... if you have the Spiritual Skill Bundle then you're some kind of priest or maybe a Bard or therapist... I took the concept of the Primes and tied them to specific actions that occur in games (basically I deconstructed the "classes" from C&C and turned them into a bunch of skill bundles that you could then mix and match to custom build what you want).
But at its heart, the original SSEH was a toolkit... it presented options to let the group build the game they wanted to play. 2nd Edition will not be any different from that... there are "Tweaks" provided to help groups tailor the game they want. If you want Mutations (like from Gamma World) then there's a Tweak for that... if you want Cybernetics a la Cyberpunk 2020, then there's a tweak for that... it's designed to be modular in its approach to the rules. There are even tweaks for dialing back in "more C&C" like putting back in the traditional D&D stat line or using Levels instead of Skills... it's designed to give the group the power to put together the game they want.
And the biggest part of it is the ability to build things. To me, much of Sci-fi is about the trappings. It's about the Stock Light Freighters, the lightsabers, the Vipers... so the game has a straightforward ruleset to allow groups to tailor build items, weapons, tools, armors, vehicles, mutant powers, psionics, and special abilities... and they all follow the same single rules. As such you just have to learn one path and can build whatever you want... and it's presented with a consistent rule set to balance the items built. Basically I saw games like Traveller and such that have rules for building spaceships, but if you wanted to put together a new fighter or build your own weapon you were either out of luck or needed a different set of rules. In SSEH you can build whatever you want and it all follows the same rules. Same thing goes for creating your own alien races and such... they follow the same rules.
The game will provide plenty of examples and starting equipment and ships as well as examples of how to quickly modify the provided equipment/vehicles to tailor them to your setting without needing to reinvent the wheel if you don't want. The Troll Lords have asked that the core book be setting agnostic, rather than include the original setting provided in the boxed set with a later release going into the provided setting of Victory 2442. As it stands, SSEH 2nd Edition is going to be as ready to play from the outset as I can make it... you'll just need to plug it into whatever style of sci-fi you want to play.
I think the real issue with making a generic sci-fi game over a generic fantasy game is that there really isn't as much of a "Generic" sci-fi setting... generic fantasy needs to really feel like some Vance, a dash of Tolkien, and a little bit of Howard and Burroughs and some old myths and you have a pretty generic fantasy realm... Sci fi can encompass Mary Shelley's Frankenstein, Gibson's Neuromancer, Dick's Do Androids Dream of Electric Sheep?, Star Wars, Star Trek, or the Terminator films... there isn't a set generic feel to a sci-fi setting... the closest might be traveller, but even if you look at that there are a bunch of weird assumptions beyond golden or silver age sci-finess. So, I went the toolkit route. Rather than trying to create some generic sci-fi world that can't possibly be done (do you do Psionics or leave them out? What about cyborgs? Mutants? Medical Abominations? Weird Science? What do you leave out?) I created a unified toolkit to let players add and subtract what they want from their settings... Want to use this to play a game about the Colonial Marines vs. some Xenomorphs... got it... want to recreate Star Trek? Go for it... so it will require a little work from the end-user, but the trade off is that you really would only need to learn this one game to play all kinds of sci-fi stories.
I've gone on long enough about all of this. I'll try to post some more sneak peaks as I get things that feel like they need to be seen and I'll definitely let anyone know who PMs me their interest in the playtest when it's ready.