Okay .. you brought up some interesting points about alternate races and factions. Having build several race/ship list mods, let me offer you some thoughts on the subject.
Tim's focus is on VGAP 4.0 now - he's not gonna spend any significant time working on VGAP 3.0. Some players have already moved on to 4.0, but a great many of us don't care for the new version ... which is why we're here. There's an older forum thread about our criticisms of 4.0 if you care to read it.
So ... we're pretty much stuck with the basic structure of 3.0. About the only significant change to 3.0 that Tim's done was HOST 999 and related apps. HOST 999 moves the ship limit from 500 ships to 999 ships. Unfortunately, many of the 3rd-party front ends more experienced players use don't support 999 ships.
Your point about "series worthiness" is a real tough one. When Time was building VGAP 2.X and 3.X (late 80's??) - Trek, SW and BG were the big dogs, so his choices were obvious. Now not so much. Many of us - and I definitely include myself - are B5 fans. But now we have a variety of media to choose from. From SF books (Weber's "Honor Harrington" races), PC games (Wing Commander series), as well as SF TV and Movies (The New BG, Firefly, Andromeda, etc). How do you choose?
Your point about balance is also problematic. As other players have mentioned in other forum threads, everyone has their own opinion about what is balanced and what isn't. A short review of the new shiplists forums shows the variety of opinions. My main gripe with Tim's default list is that every race has a bunch of ships that serve no real useful purpose and are rarely built. Which was one of the reasons I took to building race and ship list mods.
If you look at my Star Fleet Battles mod, most races have the same rough progression of ships - Frigate, Destroyer, Cruiser, Battlecruiser, Dreadnought on the torp side, Light Carrier, Carrier, Carrier on the fighter side, rounded out with a smattering of common freighters and alchemy ships. One criticism - a fair one - is that the SFB ship list for each race are too common; that it's basically, the same shiplist repeated 11 times. To some extent, that's done on purpose. The Star Fleet Battles board game - which my shiplist mod is based on - is very much set up that way. Many of the race differences in the board game are reflected by the weapons each race uses - but unfortunately, there's no way to replicate race-specific weapons in VGAP 3. Which brings me back to the main point - balance is a very tough thing to hit right. Make a list too balanced, and you take away some of the flavor of each race.
My answer to the balance-vs-flavor issue is to focus on the theme of the mod I'm working on. SFB is more heavily balanced because that's the way it is in the source material. In my Alpha Quadrant mod, I still have an underlying level of balance, but made a conscious effort to have more race-specific ship types. The major powers - Fed, Klingon, Romulan, Cardassian, Ferengi - have more standardized ships, but others have more variety in their lists. The Borg and Dominion are different because they're invaders to the AQ - in their home quadrants they are the big dogs and have developed their shiplists independently. The Orions, Maquis and Tholians are smaller powers with a more focused fleet. Therefore AQ is less "balanced" than SFB, but still allows each race a good chance at winning - assuming the player uses his ships and abilities smartly.
You've mentioned here and an in other forum threads about including B5 races into Tims list. What races do you take out? In Tim's list, you've got 7 Trek-based races, 2 SW races and 2 BG races. The obvious choice is to replace a couple of the Trek races. However, the Trek races are primarily torp races. B5 races all use fighters as much as SW and BG. Not a major obstacle, but one to consider. Another point, which ][avok mentioned, is when you're building a new race and shiplist, you have to remember you're stuck with the way HOST treats the race your replacing.
For example, if you decide to take out the Lizards and replace them with B5's Narn Regime. That's a fairly straight-forward replacement - both are reptilian-based races. HOST's special ability for the Lizards work fairly well for the Narn - HISSS and 150% combat damage. Now, you've got to deal with the fact that the Narn now share several Federation ship classes. Removing those ships is the obvious answer, but now you have removed an important ability - the Loki's decloaker.
And I'm not going to go into the really difficult part of building mods - finding the graphics, rendering them for both DOS and WINPLAN, then balancing the ship stats so they aren't imbalancing the game while adjusting the checksum balances Tim incorporated into the game ...
"Any ship can be a minesweeper ... once!"