Yes I get that sometimes certain Pokemon are way better with their Megas, but I'll delve into some of what makes them good. Most appreciate either the stat boost or the change of ability in some cases. Sometimes this makes the Pokemon Uberly broken, like in the cases of Gengar, Salamence, Kangaskhan, Mawile, Lucario, and Blaziken. (Get it? Because they're in Uber tier).
Maybe not Salamence so much with ability, but everything else above in Ubers is factored into that tier because of their ability, at least partially.
I think the change in ability is really what can make or break a Mega Pokemon for the most part. For instance, if Mega Houndoom had a better ability than Solar Power, which is practically and utterly useless, it might see more play. Houndoom is probably the only real waste of a Mega Ability that I can think of. Most Megas usually have a better ability when compared to their base form.
Some have an amazing stat boost to back it up, and something to support it sometimes. Like in the cases of Lopunny, Medicham, Pinsir, Metagross, and Lucario, the first two can get a free turn with Fake Out, otherwise forcing a Protect, and the latter three can revenge kill with STAB moves, for an equally free turn to give them a much needed Speed boost.
Other Megas are great because of their combo pieces to their movesets. For instance, Kangaskhan, Slowbro, and Sableye. Kangaskhan can go into a Power-up Punch, which with Parental Bond turns it into a Swords Dance immune to Taunt. Slowbro can use Calm Mind, and Slack Off, which when paired with Shell Armor make it a practical wall, and scratching off any hopes of a lucky crit. Sableye, with Prankster and due to the game mechanics, can Mega Evolve AND get priority off of Prankster for that turn with Calm Mind or Will-o-Wisp and in turn screwing over with Magic Bounce.
Strictly speaking, this is what makes Megas more viable than their bases imo.
If I wanted a Mega moved to a different tier, I'd want Lucario back down to OU. A lot has changed since X/Y, and I get that it can have different sets and whatnot, but some of the new Megas of ORAS, particularly in OU, can run circles around both sets like nobody's business. (I speak for Lopunny, Metagross, and Slowbro from what I can think of currently, all of which have a way of walling or creeping around Lucario in some way). Lucario to me nowadays is still great, with those stats and ability, but it's outshined by other Megas imo, and it's ban in X/Y while righteous, was a one-way ticket aboard the HYEP TRAIN.