If you have to pick one rule base, that's easy you go with Vanilla BB2k1 rules like are used by MBBL league at
http://www.midgardbb.com . Basically the LRB are the rules.
Regarding the Goblins: I think its stupid to waste cool features on a team that is not competitive and therefore not playable. I know what you mean with the fun aspect, but i can asure you no one would choose halflings to compete in a league.
Toby ... I think you are mistaken in your belief about stunty play. This link is for the team that I am currently playing to compete in the league that I play:
http://www.midgardbb.com/MBBL/Season1/IronChefs.html
"no one would choose halflings to compete in a league" ... another example from the MBBL2 league:
http://www.midgardbb.com/MBBL2/Season2/ ... arger.html
and from the PBeMBBL league:
http://www.mycgiserver.com/~VikingCGI/p ... rkings.htm
Three leagues, three halfling teams.
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Also I agree with Neominal. Your project does sound a lot like mixing the upcoming NAF organization with SkiJunkie's Java Client which only uses one rules base ... and for a sit-down and play client ... SkiJunkie's program is slick!
As for inability to allow house rules, well that's pretty far from the real. It all depends on what you want from the program. SkiJunkie's program is one rules base. But the PBeM tool is so flexible that it can handle the MBBL (LRB rules only), the PBeMBBL (3rd edition rules with Compendium/Citadel Journal extras), and the MBBL2 (LRB with 76 allowed different BB teams, On-pitch spellcasters, and over 20 new skills). By handle I mean, you set up the rules base and it adapts to the game you wish to play. So it all depends on how you want to write the program.
As for your final point, team management. There are no official rules for this agreed and I'm not sure if there should be. Online leagues that allowed player trading would quickly spiral into the abyss. It would not be difficult for me to play 5 Orc teams under 5 different accounts and then trade the players after several matches so that I have one team that has all players who have avoided aging and niggles and have multiple skills. My TR will suddenly soar ... fine by me ... unless the handicap rolls get me, I'm going to level someone. Also trading players is not like trading items. I don't think I'd ever trade a player for someone else's player as I take a lot of joy in building my team, having someone's work on my roster would annoy me ... I could be only on this one, but I don't think so as a lot of the argument against aging was ... "OH NO!, my Star xxx that I've been building for 2 seasons just got -1 ST ... you've destroyed my baby!!!!

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Basically I think you underestimate some of the tools already out there or on the way. The NAF is going to be creating a database of coaches. SkiJunkie's program has a great way to allow sit down games and the PBeM tool allows for people with only 10 minute allowances to play the game as well. And we aren't talking little scope here. Look at the 2 largest PBeM leagues: the PBeMBBL (50 teams, 24 coaches, 10 countries) and the MBBL2 (80 teams, 50 coaches, 14 countries) ... those are pretty decent numbers for creatig a community. If you want to go IRC, the OLBBL is massive.
Your idea of software that would allow a coach's room and then a playing field is interesting, but I think you are starting with some wrong ideas about things that are broken/unbalanced in a game that's been fine tuned since 1986.
Galak