Well, one of the big problems with Civ4 in terms of accurately portraying the differences and limitations of different types of ships is that range isn't accounted for. Between an oil-powered carrier and a nuclear carrier - or between a diesel-electric sub and a nuclear sub - the most striking difference is that nuclear vessels can be deployed anywhere around the world, at an unlimited distance from their home port, for extended periods of time.
Agreed, not a whole lot one can do about that in Civ4. However, uranium is harder to come by then oil, so I'd say it still makes nuke ships a little more special, even if they don't have much other then the fuel source as their only in-game differance.
that is what I like about the idea

I too do not like to have fighters on carriers only, and with the introduction of carriers and supercarriers I am thinking about allowing jets and bombers on supercarriers but not regular ones.
Allowing bombers on carriers is not a good idea IMHO. It's just something you don't do. To allow for the changes, I just nerfed the WWII fighters combat vs naval units, and gave a bonus to light bombers & jet fighters vs naval units. The USS Nimitz does not scramble B-52s or B-2s against enemy fleets, that's just nuts... the Nimitz would launch F-14s (formerly) or F-18s (currently) carrying some smart/bomb/missile packages. A Mirage 2000 with an exocet missile is just as dangerous (if not more) as a B-1 bomber to an enemy ship... ask the Brits.
I agree, no need for a 3rd unit type, maybe allow upgrades to either jet or bomber ?
The light bomber did re-evolve back-into the modern jet fighter... not the big strategic bomber. Today's modern multi-role jets perform the same missions as the light bombers of WWII. Neither the WWII light bomber nor the modern multi-role fighter perform the same mission or have the same capacity as the strategic bomber in regards to massive strikes or carpet bombing. Light Bombers and today's multi-role jet fighters perform more precise attacks against specific targets, where-as the strategic bombers of WWII and today are capable of massive collateral damage.
Frankly, the WWII light bomber is a much closer cousin to the multi-role jet fighter then it is to the large strategic bomber.
A final "benefit" of adding Light Bombers to the WWII timeline is that it forces carrier users to seperate attack and defense roles amongst the aircraft carried on-board... just as they did in history... you have the best attackers, the light bombers and you have the best defenders, the fighters (it was important to "nerf" the WWII fighters naval attack value of course!). With a capacity of "3", you'll have to choose between how many offensive and defensive aircraft you carry on board. With the Supercarrier, comes multi-role jet fighters (with a naval attack bonus), and there is no more need to carry a mix of units... just a bunch of multi-role aircraft. With a capacity of "4", it's like having four fighters and four bombers... instead of having 1 of one and 2 of the other in WWII. Simply put, adding the light bomber to the WWII timeline just forces more strategic thinking in what you want to put on carriers or build in your cities.
I went the opposite direction, introducing WW2 carriers as early carriers (with less capacity) and keeping the regular carrier as the supercarrier. I will probably stick to that theme, but increase the capacities of both carriers and move the regular one a bit up the tech tree, so it doesn't follow right on the heals of my early carrier.
The exact same stats of the original carrier remains the first carrier... except the "default" graphic is Snafu's Langley, and of-course any WWII flavor carriers go to their nations (Japanese, American, German, etc). The new stats (larger defense and capacity) go to the supercarrier with a later entry date (Advanced Flight and Fission). One has to remember I also added "Air Superiority" as a new tech in-between Flight and Advanced Flight, so there's a little extra cushion there too to give plenty of use-time out of the first carrier units... and maybe it's just me, but I never seem to be in a hurry to get advanced flight anyways... I can do a lot with the WWII fighters and bombers.
Nothing wrong with the direction you went, just realize you actually delay what Firaxis had in-mind... a 3-capacity carrier at the advent of flight... you now have to wait longer for. I just left the Firaxis carrier mostly "as-is" and added a later supercarrier with a beefier defense and slightly larger capacity. Either approach is feasible though.
I say whenever you have a new version put it out, people can always d/l it when their games are done.
Yeah... I'll probably release this within the next 24hrs... with a big fat warning it will trash your current saved games!