Wow, lots of ideas. Comments follow.
1) Allow all players to complete all of their matches anytime during the posted "season" amongst themselves since some have busier months or weeks than others - vacations, sick times, kids, events and the like.
Though not explicit, our format allows this to happen, it just does not encourage it. My belief is that most members will benefit from a schedule and because of it will tend to "keep up" more or less.
2) Have everyone pay up front for the entire season (or offer other payment ideas so you don't have to make any trips to any club just "to collect") before match ONE. How about allowing PayPal gifting directly to you as one possible way to get everyone's full season "deposit" so to speak in before kick-off. We know this was once called The Gentleman's Game, where your word was all that it took to guarantee a full season of commitment - maybe we can change that a tad to reflect modern times and refer to 14.1 as The Modern Man's Game ;-)
I thought of that, and was concerned that too many would balk. I was more interested in getting a high participation and let that influence me. I thought the "deposit" idea would be a good compromise. We'll see. Paypal, or something like it, is on tap for the future as part of a fully automated website.
3) Since no particular club would now be holding fees collected, that opens the door to even more flexibility and other location "adventures" on any size table as long as both agree. You could have an accurate compiled list of possible club choices with tables and pocket sizes, rates and club prices and times/food specials, etc. It could also allow players to even host a few games on their own table if the other player agrees. I know a few friends that have some beautifully set up 9' GC's that I'd play on any day. There's even an 8' table with Mosconi record-run sized pockets that some may want to try.
I myself would have no issues re:what tables the players agreed to play on. It's one more thing to potentially disagree about, but in practice I think it's not likely to be an issue. Playing at someone's home would be interesting, and if offered up as a venue by the owner and accepted then I'd be OK with that too. What if, though, after arriving the nonowner discovered it wasn't to his liking, the cloth was crappy or the wall was too close on one side? In a cheap league these would be small points, but with serious money at stake, people can get very persnickity.
4) Trophies. Small but still a trophy. Goes along with the prize monies of course. Optional if they don't want to take it but not taking the trophy for whatever reason doesn't get them any more money - it simply passes to next sessions trophy stash - engraved plates for the trophies aren't set until the last match is competed and winners announced anyway.
I don't think this would be worth the money for most of the participants. A plaque, which could be updated every season with that season's winner would be better received, I think, but where would we hang it, if we're playing all over. A virtual plaque on the future website I mentioned above might work, it'd be real cheap

and always available for anyone to see.
This idea might work much better in a bigger handicapped league tied to a specific pool hall. Trophies might go over better, but I think the plaque wins here as well.
5) Cash prize for Highest RUN or possibly even Highest BPI in addition to the top few finish players based on Won/Loss record during the normal season.
As to BPI, I don't know how receptive the high skilled players would be keeping detailed data about every game. I didn't ask, given my experience in two handicapped leagues (with players of widely varying skills). Maybe they'd feel differently. As far as paying out for a high run, that would be fine for seasons 2+. I just wanted to keep it simple the 1st time out.
6) Have the per-match fees lower and have a double Round-Robin setup ---- or even make the season end with a playoff series held amongst the top four finishers and those players then are guaranteed a cash payout. Pay 1st through 4th. Like a single elimination quarter/semi-final brackets with matches to 150 and the Final a best of 3 or something. That would be 7 Matches (of say one frames each for the Quarters/Semis and best of 3 for the Final) and those match monies collected from those 7 matches goes to buying the trophies - or increasing their own prize fund.
I purposely avoided having a playoff, even in the event of a tie. Here's how I explained it to the players:
The winner, 2nd and 3rd places will be determined by number of wins. In the event of a tie, Total Balls will be the tie breaker, so even if you are way behind, every ball counts. If there is still a tie, whoever won the head to head match gets the win. Play-offs would make more sense in a league tied to a venue.
7) For scoring, have "the League" members use an electronic phone/pad scoring app that they can forward to you for stat keeping and determining records as the season progresses. Again, no reason to make a drive to collect monies or score sheets. The Modern Man's Game
I like this, and would be happy to do it. Not all my players would. I have a person without a cell phone, people without smart phones, etc. The most interested in this league were the old guys, not all of whom want to fool with this "modern" stuff.
My limited use of a scoring app I tried out on an Android tablet was fun but frustrating. All the mistakes, poor error handling, I wasn't impressed. Not bad for nearly free, but not good enough to require where $thousands are at stake. Maybe they are better now, I'm sure they could be, but again, I just kept it simple. I provide a blank Match Result sheet they get from the pool hall which has places for the date, location, names, scores, high runs and signatures of both players. Asking more than that at this point in my project would just unnecessarily complicate things with very limited reward.
Once successful, I'd like to introduce things that would streamline the process of collecting the money, making the match appointments, and gathering/massaging/publishing the results.
Thanks again for your input. I like a lot of what you suggest but went with the KISS principle for now.