Typcially, TKTS comes out a bit cheaper than discounts IF there are discounts for the top priced tickets.
TKTS HAS to give you the best tickets available to them as you buy them. So you'll often get better seats than through discount. But if you're happy to sit in the back or mezzanine in a cheaper prize range you'll be better off with a discount.
With the TKTS you can only buy on the day, while discounts let you buy in advance.
So there are your pros and cons. I've done both, although TKTS more frequently this season as I felt most discounts were "only" 30%, last year I had quite a few that were 40%...