Carriers have numerous advantages and disadvantages. The biggest problem they face is that they're just too easy to run down and kill with frigates. Light frigates in particular are fast enough to close the gap before you can blink, and early-game this is going to put a quick end to your carrier-based strategies. In the late-game, huge swarms of strike craft get countered by the right capital ship abilities. The Vasari in particular can completely shut you down with jam weapons and phasic traps. Advent and TEC will punish you with TK push and flak burst respectively. Going pure carrier is just asking to get countered. If you can substantially outnumber the enemy this is somewhat irrelevant, and carriers (equipped with bombers) are definitely the game's best coup-de-grace unit. However, for a straight fleet battle I'd be inclined to mix unit types thoroughly and wouldn't want to lean too heavily on strike craft.
As for the best carrier, they're all roughly equal. The Advent carrier has better range due to its larger antimatter reserves (this scales nicely with the larger unit size) but otherwise they all cost and perform about the same. Now, as for strike craft, the biggest difference is Vasari, which uses the phase missile type weapons for both its fighters and bombers. This makes them incredibly effective against anything that has shields, and absolute monsters against capital ships. When fully upgraded, Vasari fighters are better against capital ships than the other faction's bombers.
If you really push it late game and can max out mass transcendance, the Advent Halcyon becomes an extremely nice carrier. It can swat away enemy strike craft with its TK push, and offers six squads thanks to its adept drone anima. Level it up once, and now it's fielding eight, outpacing an equal value of carrier cruisers, and level it up twice and anima tempest will really make your day. Of course, I've almost never seen it done in multiplayer.