It was deserted because there was no fast way there. The monsters in eos tower and omega are/were the most unique in the game, even today. Eos tower is awesome, if it had a 100 level boost like other other crap places post big bang, it would be a very popular place to train.
@ulieq it was deserted because the quests were mediocre and there were better training spots around at the time. Eos tower scrolls got you there pretty quickly, and then there were also the Ludi/Omega warp capsules you got from a quest iirc.