Well, invisibility's nice and all, but its significance is lessened by the fact that you'd be damn near 'invisible' already by the time you get to such a spell. Muffle's already covered by a perk in the sneak tree and equipment if you choose to wear that kind of stuff. If anything, the biggest advantage with illusion would be calm/fury etc. You'd have quite a lot of control over your encounters, so it'd both help make you feel less overwhelmed in a straight up fight, and allow you to pretty much set up an assault in your favor beforehand by picking people off without lifting a finger. If you're not leveling restoration, the courage spells also get companions up on their feet after being downed. Doesn't restore their health by much, but its enough to regain support or a distraction for a bit if things get hairy.
Alteration is great and everything, but there's a shout to detect life already. Detect dead seems pretty useful, but when you consider how most undead are draugrs that are scripted to wake up and/or burst out of coffins, you'd be able to get the drop on them most of the time anyway. Though I guess there are vampires and such.
Alteration in my mind is useful simply for the shield spells, awesome magic defense, and paralyze. All three of which you wouldn't exactly need for a thiefsassin, even if they are rather nifty. :V