It took me a bit longer than expected to assemble the unit stats from the .biq, but now I can present you my first suggestion at unit tweaking. Please see the zip archive attached. It contains three Excel/Calc spreadheets. They are done with OpenOffice but stored in Excel file format, so hopefully opening is not a problem for you.
The first file, Star Trek Units, is a list of the units as they are currently contained in the .biq. I did not import all units: I did not find barbs or other irregular units interesting. The units of all main players are completely contained, however.
The second file, Star Trek Units 2, contains the same units, however arranged by function and era to give a better overview of the ships available to the different civs at different times. With this overview it is for example quite easy to realize that unit distribution is uneven. I.e. the Klingons lack later units, while the Cardassians lack early units. This is certainly explainable by looking in which shows the respective Races were featured most, but still I think this needs some balancing. The roles attributed to the ships seem quite random at times, too, with Destroyers and Command ships sometimes having nearly the same values (i.e. Steamrunner and Galaxy). In addition some race modifiers seem to me not very sensible, for instance the fact that Dominion units have generally one hit point less (including the big and powerful Battleship!), while the Jem'Hadar ground units have a Movement of 2, giving them the possibility to retreat when losing, which is not justifiable by anything within the show. To the contrary, the Jem'Hadar are among those fighters least likely to ever retreat: "Victory is Life!"
The third file, Star Trek Units Workshop, contains my own suggestion for the units. I did not tweak the units individually. In fact I did not touch the stat of even a single unit. Instead I created a small set of relatively simple formulas which calculate all necessary stats out of Race, Role and Era. I did explain these formulas in detail in the file, so I hope that whoever is interested in what I have done will not have too much difficulties understanding them. The formulas use a lot of parameters which can be easily changed. For instance modifiers for every role or race. So even if you do not like the parameters that I have used you could still use the formulas with different parameters.
I did tweak the units I found in the file. However, it might be sensible to modify the unit selection since it is a little bit uneven distributed as I stated earlier and you can see for yourself. I did not try to correct this at the moment, I was solely concerned with the existing units.
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My suggestions rely on the following assumptions: There are no shuttles (anymore), the only units are ground units and space ships. Now my idea is that bombardement is used mainly to damage ground, not space units. To meet this end I made the unit stats of ground units significantly smaller than those of space units. Bombardement strength was reduced as well, so that the chance to damage a space ship is small, to damage a ground unit fairly high. My next suggestion is to make bombardement lethal to land units, but only to them, and to also reduce their hit points, to make bombarding them even more effective.
My next idea is to roughly divide units into small attackers and defenders as well as big attackers and defenders. Additionally scouts and transports, of course. Small attackers and defenders are the standard ships for a given era, with the small defenders having the same (small) attack and defense value, while the attackers have a higher attack but a lower defense. The big versions have a bit higher stats and an additional hitpoint, but are much more expensive than the small versions. My aim is to make it cost efficient to rely mainly on the small types and only occasionally build a big version, where the extra firepower or defense is needed. This matches roughly the distribution of Cruiser, Destroyer, Command Ship and Warship. Only the Heavy Cruiser is not matched directly, but I think while this differentiation is nice, it is not really useful, given the limited amount of different ship designs.
I gave the bombard ability exclusively to small defenders, who now have the additional role to prepare ground invasions. The big attackers have additionally the blitz ability. Giving the small ships bombard ability and the big ones blitz has two nice effects: Lots of small ships can now destroy big ones effectively: Their (when applied to space ships) inefficent bombardement ability can nevertheless finally reduce the big ship to a level where it can finally be destroyed in a direct attack. The big ship on the other hand has the ability to take out several smaller ones within one turn, making a strategy possible where one relies only on the big guns, which would not be possible otherwise: One would simply and unrealistcly run out of attacks, no matter how much superior the own fireower would be. I did however carefully avoid giving a unit both blitz and bombarding abilities, because I think this not only overpowers units but also does not reflect the Star Trek space fight situation where space ships engaged in fighting always damage each other. The bombardement ability of small ships however reflect the situation where more small vessels attack a big one than it can handle at the same time.
I did not try to reinvent the units, I tried to use what I found without destroying the spirit of what had been done before.