Since I have leveled all 3 as healers, I'll chime right in
Questing/leveling is a breeze. Your damage output even as a healer is quite decent. Since Mercs are mainly tank healers, you will have no problems keeping your companion and yourself alive even in difficult situations.
However, healing Flashpoints is tricky on the Merc. Most difficult healer to play in the game, due to an unforgiving ressource management. Managing heat means "one error and all is lost". Once you learn how to handle your heat Merc gets manageable, but it's nowhere as easy to play as an Operative.
Companion-wise, I went with Gault as soon as I got him, right up until I got Torian. Torian is the bestest companion for a healer Merc. I did go with Blizz for a long time, but just because Blizz' personality is pure awesome. Seriously, Torian's where it's at.
for solo PvE it's a mixed bag. Like with the Merc you're basically immortal. However, you don't even get close to the kill speed of the Merc, especially on mob groups. Where Mercs can just AoE everything to bits, the Operative pretty much has to pick off targets one by one. And the single target DPS isn't anything worth writing home about either.
For companions, I think Agents don't get anything too useful there either. I went with Kaliyo all the way, since Vector is far too squishy for my liking. Tried Temple for a while, but somehow that didn't work out too well either. And because I'm to cheap to buy/build parts for Scorpio I'm still stuck with that insufferable little Ratataki. Which in turn really doesn't help kill speed.
On the plus side, Agents are super easy to heal Flashpoints with. Keep HoTs rolling and add a Kolto Injection every now and then. In your mid-twenties Energy won't be much of an issue either, since you can regenerate quite a bit with Healing Scan.
Sorcs for me are kind of middle of the road. I felt you had to work more to keep yourself/your companion alive than on the Merc or Agent, but the DPS is better than the Agent's. Kill speed is definitely on the good side. In your mid-thirties you will get your lightning AoE and Ashara, making you pretty much a soloing machine. While Ashara is not as good as Torian (she uses Marauder gear), she does pretty awesome damage.
For Flashpoints, Sorcs are very straightforward. Huge ressource pool to work with, but once that's gone, it's gone. If you have ever played a Holy Priest in WoW, this basically is what Sorcs feel like for healing. Not the best at keeping a tank going, but awesome for group healing. Which in turn makes Flashpoints a breeze, sicne there is a ton of AoE flying around.
Hope that helps.