When in doubt, pick the ship you like the most and maximize it's abilities so you have the most fun you can squeeze out of its hull.
This is my advice to people as well. Ultimately, flying what seems like 'da mostest powerfil ship in da gamez' is going to ruin your game if you'd rather be flying something else. If you really like a particular ship, that is reason enough all by itself and you will likely fly it better than another ship that you might feel isn't what you like.
The Assault Cruiser and Excelsior are close enough in performance that it really does come down to which design you love most (unless you have a definite need for the Transwarp Drive of the Excelsior, of course). The differences in BOFFs do contribute to the decision if you want to have the option of running another ship, as the Assault Cruiser lets you slide in a BOFF crew tailored for Escorts easier than the Excelsior (which is more geared towards Cruiser BOFF setups). If you haven't purchased additional BOFF slots, you will likely face either picking the one with the number and type of BOFFs you have, or having to drop BOFFs to fill the new slots (or leave one or more vacant).
Still, the most basic reason is the one already posted. The Assault Cruiser is the 'standard' tactical cruiser and can be purchased with either a ship token or straight-up dilithium within the game. The Excelsior is the optional C-store tactical cruiser that must be purchased with additional real-world money. Aside from the Transwarp Drive, I don't consider the Excelsior to be different enough from the Assault Cruiser to merit the points spent unless you love the look of the Excelsior more than the Assault Cruiser (enough to pay for it).