The main problem with most game software companies by now is that they are way too much about franchises/profit and very little about creativity. I suppose this was brought largely by the monopoly of the PC since the early 90s, cause prior to that most computer game companies were smallish but highly prolific and artistic, and the games from that era reflect that (not much chance there will be a nea 'Another World' ever gaining momentum).
Not so sure why you view game developers/publishers maintaining a franchise a being a bad thing. Despite being part of a famous and well established franchise, Skyrim was a very innovative game -notably with the Radiant AI system- but also with the complete overhaul of the skill and stat system inherited from Morrowind.
Sure, some franchises have become very dull, but even within them there are some very interesting things. (According to my roommate the Battlefield multiplayer system has made a lot of very good and interesting changes.)
The internet obviously also changed things. For starters virtually all strategy games produced in dvd form are now 3d-engine based, while freeware online/opesource strategy games tend to be 2d/2,5d.
Out of curiosity, what is wrong with a 3d engine for strategy games? Technically, anything a 2d engine can do, a 3d engine can do -often better- and with more options.
I'm no stranger to 2d strategy games, yet with one exception (Disciples II, if you are interested due to the abomination that was Disciples III) I feel the game would have been better had a relatively modern 3d engine been available.
For computer games, I would love to see an RPG in which I really feel like my character is a driving force in the developing story. I want the world and characters around me to be reacting to me, and it's not just me reacting to them. For the most part, when I play RPGs I feel like I'm just being told a story, not making choices that effect the plot, the setting or the characters.
Have you tried Alpha Protocol? If you can look past a poor combat system and an ugly/uninspired art direction you get a rather neat story where you do feel like you are controlling it. Also, most of the bugs have been fixed so you no longer get the infamous 'screwed her brains out' bug.*
Also, although you say you aren't a fan of swords-and-sorcery RPGs, I do highly recommend The Witcher if you like the story-based RPG in a very interesting setting.
Lastly, if you are more interested in an inventive setting than driving the plot, you might be interested in Geneforge (mages have discovered genetics and use it to create fantastic monsters to serve them) or Avernum (criminals and outcasts are sent to a gigantic series of underground caves where they scrape by).
*There was one romantic encounter in the game where if you chose a certain set of dialogue options, you would get stuck in a loop where she would endlessly repeat the exact same dialogue over and over and over.
@Gori: That sounds a lot like a simulator game, have you tried Mount and Blade?
EDIT: Interesting article on the 'indie bubble' by Jeff Vogel. (The guy behind Spiderweb Software, which produces ultra-low budget text heavy RPGs that make the original Baldur's Gate look graphically advanced.)
http://www.gamasutra.com/blogs/Jeff..._Luck_and_the_Popping_of_the_Indie_Bubble.php
tl,dr: There are so many indie games out on the market they are encountering the law of supply and demand and are selling their games at a super low price, often earning less than a dollar as profit and creating a state of affairs that ultimately can't last.