From the research that I've read up on, it seems that the Mortis Engine is more useful. Boosts spellcasting, debuffs enemy spellcasting, and the ranged Wail of the Damned will affect ALL units within its range (though that attach is based on Bravery, so only low Bravery units will really get affected). Also, the one-time Reliquary bomb is has seems pretty useful as well, as you'll generally roll 12" range or larger.
The Command Ability of the Coven Throne is pretty worthless, I think, but you'll likely not use the Throne as your General.
The Blood Kiss ability sounds cool, and would be a neat way to add a Vampire Lord to your army - but in Matched Play that's the problem - it ADDS to your army, so you have to have points set aside for the Vampire Lord that the Blood Kiss attack could POTENTIALLY make.
The Throne has the Vampire Queen atop it as a Wizard, and the Mortis Engine is not a wizard, so the Throne has that going for it - and the special spell the Throne has is not that bad, as you can hold up a part of the enemy with that spell going off.
Overall I think the Mortis Engine's abilities and buffing ability towards your other wizards is good (assuming you are using some kind of Wizard in your army, of course). I believe that the Engine is cheaper points-wise than the Throne as well, so that helps out if you're doing Matched Play.
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