I think you're exactly right in that they made it into a 'nameless RTS'.
If you think about it, if they renamed Supcom II to 'Tactical Demigod' or something, people wouldn't be complaining half as hard since they wouldn't be comparing it directly to its predecessor. The game does fairly well as a generic RTS, but that's all it's going to end up being, a generic RTS that doesn't really make any waves on the game front. It's missing most of the features that made Supcom what it is.
That being said, those features are (hopefully) not gone, just buried under a surface layer. If we can strip that surface away entirely there's lots that's great about the engine itself.