The transition to F2P couldn't really be hancled any more differently than they did for CO. With CO it seems the consensus is that current subscribers got a pretty good deal, were treated with respect, and overall F2P enhanced the product. People can play for free but there is still incentive/value to maintaining a sub, and nothing was really taken away from current subscribers.
For STO, current subscribers have been wholly reamed up the ass, with a minimum of 30% of their current assets "stolen" by Cryptic via their conversion formula to the new economy. If you are very wealthy up to 60% or more of your total assets could be lost in the currency conversion. That represents nearly a year or more of play for longtime players, who ironically, amassed such great reserves of wealth because there has been literally nothing new to do in the game for the past 11 months except grind daily missions for wealth.
Repeated promises of "nothing will change for subscribers", "you aren't going to lose anything" have repeatedly been ignored and broken in favor of more ass-reaming. They openly stated that while a few C-store items would increase in price, most would be coming down. In reality, over 80% of the items in the store have seen a price hike. To add to the insult, C-store items that used to be per-account unlocks like pets and tribbles, are now per-character. Got 4 characters? Gotta pay 4 times to get the pet on each. Delete that character so you can make another? Those purchases are erased with the character. Oh don't forget the price didn't go down as a result of this change either.
If you thought leveling was pretty ridiculously fast before, know that it actually has been made even faster. However, due to the dilithium economy, you will be stuck grinding dilithium for literally weeks and months in order to gear up. At higher rank upgrades (starting with captain I think), you actually are not awarded enough money to buy a new ship, so you are forced to grind the dilithium out (note that this only applies to free players, subscribers get the tokens like always). So there is a very awkward imbalance between being overleveled yet underequipped, until you reach max level where you literally grind dilithium for months before you can outfit yourself with the max grade gear. Of course the handy way to get around that is to buy dilithium from the exchange, in trade for Cpoints you bought from Cryptic. The dilithium economy was also devised to simplify the mess of currencies that were in the game before. Emblems, marks, merits, badges, medals, etc. it was all confusing. Well now we have just dilithium, EC, and GPL, but there's also a plethora of borg salvage/pickups you need to get the STF gear, "unreplicatable materials" you need to craft, etc. which are all essentially still currency, except this time around they also take up space in your inventory.
I don't know if it has changed in the holodeck build of F2P, but for the entire tribble testing period, you were forced to play the story missions through one-by-one. Instead of it being based on level, it is not a totally linear process. To access the already-released FE's, you have to play through all the missions, since they're incorporated into the storyline missions.
There is little value to subscribing/maintaining a subscription. It is far more effective to simply buy $15 worth of CPoints every month than keep paying for a Gold account. You get a lot more for your money that way.
Nearly everything in the game has become attached to the "real-world" currency dilithium (real world because it's tradeable for C-points, which can be bought directly for RL money). What used to be easily obtainable in-game (such as crafting) now require dilithium, meaning you either have to trade for it on the exchange or grind it out by playing- even if you are a subscriber.
Virtually no content has been added to the game with F2P, and none in the past 11 months since the last featured episode series was released. This comes after repeated promises by the Cryptic team that they were shooting for "5 or 6 series in 2011". The DOFF system is finally being released, after being delayed about 6 months (supposed to have launched with Season 4). Missions-wise, there is one single "new" mission, which is the borg ground invasion on Deferi. They "promise" Season 5 will come in Feb (which means it got delayed yet again) but nobody believes them at this point.
The F2P build of the game, now officially live on the holodeck (main) server, is still rife with bugs, incomplete functionality, and imbalance. This is after 2 months of development. I have personal doubts that anything substantial will change before they open the servers up to F2P players. The game has launched for a second time in an unfinished and buddy state.