As Antman says in his first sentence, the most important factor is whether the underroation is so bad as to downgrade the jump.
For instance, in 2007 Worlds SP Mao Asada attempted a triple flip/triple loop (10.5 base value). But she could only manage a 3F/1Lo with -3 GOE and ended up with only 3.0 points for the combination. It landed her fifth in the SP and cost her the World championship.
In the LP she nailed the 3F+Lo, got positive GOE, and ended up with 10.83 for the element.

This, along with the triple Axel, would have been enough for her to catch Ando after all, except that Mao's easier combo, a 2A+3T, was downgraded and she received only 3.4 points for it instead of the base value 7.3 (next year it will be worth 7.5).
BUT...the real reason why the CoP has killed the 3T/3T combination is something altogether different, unrelated to the difficulty of various combos.
According to the Zayak rules you can only repeat two jumps, the repitition must be in a combo, and you cannot do any jump more than twice, regardless. So if you do a 3T+3T, under the new judging system, you have cut yourself off at the knees. Now you cannot do 2 Lutzes and 2 Flips, the highest point getters, you cannot do a 3F+3T, you cannot do a 3Lz+3T -- CoP-wise, you're screwed.