It's been years since I last played the first Freedom Force. Nostalgia keeps reminding me that it's one of the best games to have graced the PC, so for fairness sake, I shall skip the comparison between this and the first Freedom Force, and just head straight to the pros and cons.
The story takes place after the events from Freedom Force. This time, the Freedom Force members find themselves against a twisted Third Reich, whose parties are headed by twisted leaders. There's nothing very special about the storyline, apart from it being retro and campy. The story is half presented in game-rendered cutscenes, and half presented in the form of comics and visual art, but it's well-done; so, despite the lack of CG, it's rather entertaining to watch.
It's quite a standard fare RPG/RTS game - if you've played them party-based RPGs of yonder ol' days, you'll roughly know what to expect. There's a Pause function which can help you manage your team better. The interface hasn't aged well though, and is rudimentary at best, but it works well enough. Just expect to do a lot of pausing to micro-manage your team.
The humour in the game is spot-on. As mentioned, the story is campy, and so are the heroes. How can one not like Green Genie's ability to change enemies into a vase of flower, or Bullet's flirting with Tricolour? The superhero powers and everything else are well-preserved, and added on, from the first Freedom Force (ok, I know I said that I would not mention comparisons), totaling quite a hefty number of animations and special effects.
Speaking of which, you can actually create your own heroes, be it using in-game meshes or fanmade ones - which are spread all over the Internet - and then take them out into the Rumble Room to test their mettle. It's good fun in that once you're done with the main campaign, you will still end up spending hours mucking around with your custom superheroes.
Freedom Force vs The Third Reich - I wholeheartedly recommend it. You just have to get used to the clunky interface.
BTW if you've bought it, be sure to download the FFX mod. Google also yields quite a lot of results for custom skins and meshes.