Only ever got to try this once (and for whatever reason failed the mission) as usually the minute I warp in the map is void of any tholians and then I am suddenly warped out back to sector space by the game.
"The world ain't all sunshine and rainbows. It's a very mean and nasty place and I don't care how tough you are it will beat you to your knees and keep you there permanently if you let it. You, me, or nobody is gonna hit as hard as life. But it ain't about how hard ya hit. It's about how hard you can get hit and keep moving forward." - Rocky Balboa (2006)
I've managed to complete it twice, but most of the times you've random guys in rainbow ships taken down by two heavy torps warping in. I'd vote for incompetence.
The unfortunate truth, this alert and the borg alerts only take 2-3 good players but the general player base lacks the ability to handle such incoming fire, I can't tell you how often I see people ignoring basic things like tac team and energy uniformity
From what I've seen, it's usually general incompetence. I've completed about two or 3 dozen in total over all my toons, and it's usually pretty obvious from the get-go if we're going to win or not.
So far the teams that have done the best are teams composed of two cruisers/battlecruisers and 3 escorts. The two cruisers/battlecruisers draw aggro from the groups and the escorts get the kills. Then each cruiser takes on one of the tarantulas and tanks it whilst the escorts clean up it's support ships, then they focus down each tarantula and tada, finished.
However in answer to the incompetence (since I just listed an example of competence), it's almost stupidly easy to get to level 50. And on your way up, you aren't taught much of anything other than the basic "use energy to kill shields, use kinetic to kill hull". Anything past that, like BOff abilities, DOff enhancements, etc, are self-learning, and let's be honest, most players in this game are idiots. They think that their builds that work in NORMAL difficulty missions work perfectly. Until they are taught otherwise in a PvP arena/ESTF. Then they become nerd-rage idiots (ones who refuse to change), or new players whom we can teach (and most of us gladly do so).
However now we must look at the Tholians. They are powerful enemies with lots of disables and are generally infuriating to fight. They keep your weapons and engines offline as a general rule, and are constantly lobbing tricobalts at you in addition to trapping you in webs pretty regularly. Even experienced players sometimes have trouble with this (myself included), so imagine if a fresh level 50 goes in there (with his lack of knowledge and only limited true battle experience and his build for normal difficulty missions). They get MAULED. I have seen it countless times. Give the Tholians the chance, and they will tear you apart. I have seen everything from science ships to escorts to BoPs to Odysseys to Bortasqus to raptors all slaughtered by the Tholians. Followed shortly by the raging about OP opponents and bugged ships.
It's actually very simple to fight the Tholians, once you get past the fact that they will make particularly STRONG efforts at keeping you disabled. They are squishy (at least their ships are when it comes to durability). They also use phased tetryon (so don't bother trying to keep your shields up, focus on hull heals). They use Subsystem Targetting (so use EPtW and ET to keep your weapons online). They also make webs constantly (so AoE abilities, like TS and BFAW are your friends). Take all that into account (plus the counters I put in), and you can win. It's just learning, which most level 50s don't do until they are forced to, and even then a lot of them still don't.