Although there should be nothing in the C-Store that will give you an advantage; you could do worse than spend some of your points on:
Federation Advanced Heavy Cruiser Retrofit: Excelsior Class
You'll need to wait until you're a Rear Admiral to be able to buy this one. But it's a great combination of Cruiser survivability with Escort punch. The combination of Bridge Officer slots and turning rate makes it the best Cruiser in the game. (Subjective opinion.)
Liberated Borg Bridge Officer
Borgarella comes in two variants; Federation and Klingon. Buying her for one faction unlocks it for all characters on that faction. She's an Engineering Bridge Officer with some nice abilities.
Tribble
The Riviera (aka 'Golden') Tribble provides a solid set of buffs when stroked. This one is also a good base for the Tribble Breeding mini game - as feeding it easily available food will create better tribbles that have particular specialities. (
More information) Klingons can't use Tribbles, but a purchase unlocks them for all characters.
Borg and Fluidic Tribbles
These tribbles were originally given away as rewards for testing earlier Seasons of the game, and provide bonuses against Borg and Undine NPCs respectively. The Fluidic one is also useful against Remans or any other NPCs with psychic attacks. I believe Klingons CAN use these Tribbles, unless things have changed. They are also unlocked for all characters.
And that's about it, really. Don't waste your tokens on character-specific services like extra ship or Bridge Officer slots. You'll find yourself switching alts until you settle into characters that suit your playstyle, which may change in future patches. If you like Uniforms, the Uniform slots are account-wide. And more character slots never hurt.
Important: I'd recommend waiting until there's another 20%-or-greater discount sale. These come along every few weeks.
Also, if you haven't already, you can get another 500 points for less than store prices by buying the Steam version today. That also comes with a lot of nice unlockable items as well as the playable Joined Trill race. (Different from the regular Trill.)