Champions Online went F2P at the start of this year.
I am not a CO expert, and I haven't PvP there at all yet. But this I know:
C-Store Buffs
1) There are several items in the C-Store that buff your character, or even change it. Heals, Power Recharges, Devices that turn your character into a different creature with different power sets.
2) These items do not work in PvP.
As the noob player of one of the more squishier archetypes, I must admit that I needed quite a few of these heals already.
Silver vs Gold
Champions Online most interesting feature for many players were the abilty you could create characters there. You could combine abilities from different power sets and were not limited to a single, rigit class structure.
For the move to Free To Play, Cryptic introduced a new type of character, an "archetype" character. These lose almost all of this freedom, and instead provide a single thematic build.
It can be argued that the "Free-Form" characters can be more powerful than the archetype characters (if you know what you're doing).
For PvP, Cryptic seperated the PvP Ques so that archetype characters would only have to compete with other archetypes (though I think you can also go into free-form PvP with them, it is probably not recommended.)
Conclusions for CO
So in Champions Online, there is no Pay-To-Win concept at work. The only buff applicable for PvP is the Acclaim buff, that means you earn more rewards from PvP. Which is obviously not affecting the actual game balance.
What does that mean for Startrek Online?
I do not know for sure.
I have the feeling that they don't actually intend to create as strong restrictions as they did in CO. On the other hand, introductions like the Rhode Island give raise to speculation that they are indeed planning for a Pay-To-Win model - at least for the lower tiers. We will have to see what is happening here.
I could see a restriction locking your career choice and your ship choice (e.g. Tactical Officers have to fly Escorts, Engineers Cruisers and so on), but that would also break apart if we think about the KDF. (Wo gets to fly Carriers or BOPs? What do Science Officers fly?)
These are the plans as far as they have been announced:
Badges, Marks and Emblens will be rolled into one currency. THis change is already coming in September, if all goes to plan. This "time-based currency" (as dstahl put it) will be called Dilithium.
All existing in-game ships will be changed to be buyable via Dilithium, not Energy Credits, Marks or Emblems. (Note that Energy credits itself will still exist.).
Ships that are C-Store only will remain C-Store only. (Unclear what this means for ships that exist in both.)
But there will be a way to exchange Dilithium for C-Points. This exchange, according to dstahl's reply, will be based on some kind of auction process, not on some kind of NPC vendor or automatic exchange rate model.
Some might consider this as a way to invite more gold farmers, but it seems that others games using such approaches did not have this happen. Quite possible that the strong competititon with many players and the legality of such offers ruins profit margins. Especially if you consider that many gold farmers only sell you cold so they can steal your credit card details - if there is a "legal" way to buy it via Cryptic, that source of revenue dies to them.
What it means is that someone
has to pay for the C-Store you want. Even if that's not you.
A relatively balanced but still optimistic outlook for me:
1) Tier 2.5 to Tier 4.5 will enter the C-Store and will remain available exclusively for C-Points.
Nothing will be done to split the PvP Queues for this. If you want to PvP at this tier, you better earn some C-Points.
2) Tier 5 remains Tier 5, no Tier 5.5 or Tier 6 ships (unless there is a level cap increase eventually.
3) Any new heals and buffs added to the game will remain unavailable for use in PvP.
A more optimistic view would be that Tier x.5 5 die and the Rhode Island remains the odd man out, and a somewhat less optimsitic view could be that they will be segregated.
I do not expect that any players will be barred from entry for PvP. This would serve no real purpose (especially not if you want to sell the Rhode Island and the like.)