I've played a few of the games that are currently being developed by the startup companies. Plenty of creativity there. Predator had some very creative modes, Full Throttle has an interesting layout. Haven't played Ben Heck's game, but that looks very creative and interesting to me. So the creativity is there, only these people are not employed (yet) by a large manufacturer.

What may be related: the smaller companies can take their time, while the bigger companies need to keep the production up and have their design teams overworked and under stress. Doesn't seem like a formula for success to me.

It could be me not getting it, but why is creativity in pinball associated with original themes? Every game, licensed or original theme, needs creativity. Else a licensed game will just sell on the name and turn out to be a huge disappointment. Creativity in licensed themes may be restricted in terms of what will be allowed with the art, but that's no excuse to not be creative with the design and find a good tie-in with the license.

In Pinball Magazine No. 1 and 2 you can read that:
Police Force was originally designed to be Batman.
Dr. Dude originally started out as Teenage Mutant Ninja Turtles.

IPDB.org probably has some notes with certain games about their origin.

I may go off topic here, but since the original theme vs licensed theme discussion seems to come up again and again, as does Gary Stern's motivation for choosing for licensed themes, let's look at two potential themes.

Let's say manufacturer A is doing a Pirates of the Caribbean game and manufacturer B is doing a pirate themed game named Captain Jack (no pun intended). Manufacturer A choose the theme because it will easily sell games because of the recognition. Some may say that's a lazy way of doing business, but others will think it's brilliant.
Manufacturer B is glad he didn't license the theme, because he would be buried in dealing with IP lawyers all the time. Instead they can be as creative and innovative as they want to be (up to a certain point) and mock the license a bit. For starters company B is marketing their game months upfront and informing potential buyers of the progress in the development of the game.

Eventually 2 companies offer 2 pirate themed games. Company A may have a jumpstart due to the popularity of the theme, but they also have a so-so reputation when it comes to reliability and earnings. Company B is a new player on the scene, but their game turns out to be pretty innovative (LCD in the playfield), fun to play and brings in more cash at locations. Even operators that turned down pinball in general are now interested in this game.

Now the biggest question: how will this scenario affect the pinball market in general?
Will it be positive or negative? Or does that depend on from which side you look at it? Will both companies go broke? Will company A raise their prices because they sell less games due to competition? Will company B sell enough games to make it as a manufacturer? Will company A get more creative in their designs now that they have to compete against something else than their own product? Is competition good or bad for the business? Does it require competition to become creative again?

Sure this is all theory, but it could be interesting to see what people think will happen.