The module that comes for free with the base DCS download is the Su-25T, which is an anti-tank variant of the Su-25. The module that is available for purchase is the original Su-25. I don't have much experience flying the Su-25, so I can't speak to the differences in the quality of the flight model or the performance of the aircraft, but as far as weapons go I do know that the Su-25T has a few more options to choose from.
Both aircraft can equip TV-guided missiles, short range IR air-to-air missiles, unguided bombs (up to 500 kg, I believe), gun pods, and unguided rockets. The Su-25T however can also equip Vikhr laser-guided missles, an IR targeting pod, as well as Anti-Radiation (SEAD) missiles and the necessary targeting pod for those as well.
Not having explored the Su-25 myself, I'm not really sure how much these differences affect its flexibility.
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As far as I know, there is no difference between the Su-25 you'd get from buying it individually and the Su-25 you'd get if you bought the FC3 bundle. Same with all the other aircraft in FC3.
The only thing I've seen that I "missed out on" with the FC3 bundle was the wallpapers. As far as I can tell, if you buy the module individually it would appear as its own icon on the main menu and you'd get a wallpaper for that specific aircraft. If you buy FC3 however, it's listed as a single module on the main menu, meaning you only get one wallpaper (it's an F-15C, btw). Obviously, since I bought FC3 as a bundle I can't be certain of what happens when you buy them individually, but that's what I understand. Pretty small drawback, but it's the only one I've seen so far.
Generally, if you're interested in more than two or three of the FC3 aircraft, it's probably worth it. If you only want one or two, it's probably not. :smilewink: