I think the reason eyebrows are raised at the DLC, besides the lingering distaste over the original ending, is the price increase that ME3 DLC has seen. At it's price, Lair of the Shadow Broker was a great value. But is Omega really worth that much more? Even if you argue that prices are increasing in general, Omega would still have to be of the same quality as LotSB. I haven't heard that it is, but I haven't personally played it.The "Buy DLC" message at the end is also gone post EC installation. And the DLC's are quite good. A new DLC is also in the works which is bringing back a ton of the voice actors and is supposed to be bigger than any DLC they've put out. Ever.
And if this next DLC is going to be so big, what are they going to charge for it? If they go for expansion pack pricing, it had better have expansion pack quality content and in reasonable quantity.
I think my biggest remaining issue with the plot of ME3 (after the fixes to the ending) is Kai-Leng. The character comes out of nowhere, has no back story beyond the "I'm the loyal henchman I'm-a gonna get ya!", and I don't really think his martial arts-movie moves and styling fit the ME universe at all. All of that wouldn't bother me too much if he wasn't there at every corner in the game. I'd have rather just seen the Illusive Man than this hollow henchman character.