The Legion lost the most, giving deference to John Byrne for a take on Superman that is or maybe isn't canon any longer effectively damaged what was a pillar of DC comics, the Legion of Super Heroes, now we are 4 reboots in and none of them have captured the magic or masses of the original run. It just hasn't been the same. The Titans are a close second, the NTT hasn't been the same for me since Titan's Hunt since then has been a string of reimaginings to retcons but it hasn't been the same either. Remember waaaaay back in the day when DC was going to start direct issue (lcbs) issues on high quality baxter paper they chose the LSH and the NTT for the titles, they were that high on the pecking order of titles. Reboots have done nothing but damage both franchises and to this day neither is anyway near it's former glorified status.

On the positive side though I loved Thomas' JSA/All-Star Squadron/Infinity Inc run, and feel that the JSA franchise might be better served on Earth Two, I cannot deny the greatness of the John's JSA on merged earth, with the reimagined Mr. Terrific and giving the JSA a pivotal role even on the 'crowded earth'.