Personally, I prefer the way Plasma was done. They acted like a organization that took itself seriously (for the most part) and plotted accordingly. Flare came off as completely silly and even at the end when Lysandre was revealed my opinion hadn't changed. Their main grunts didn't feel threatening, their scientists were uninteresting and there was no feel of connection between them and Lysandre. Say what you will about Plasma and Galactic, but I got that connection and it felt like they had their personal reasons for respecting and following their leader. Lysandre was the diamond in the rough because he was the better written character (though he had flaws), but his group bogged him down for me personally.
Well, there's a reason they act this way, mostly to the knowledge that they're most likely not fully aware of the consequences of their actions, and to the point that they're not a real villain team overall, a majority of the grunts most likely being workers of Lysandre Laboratories or those that donated to become a part of Lysandre's cause. They had a brief description, which was nowhere near what Lysandre truly had in mind. In short, ignorance was bliss.
The scientists, aside from Xerosic, most likely were not interested in Lysandre himself, but rather the outcome of his goals, the potential to change the world. They dedicated themselves to Lysandre's goal, although this is scarcely seen, it will most likely get more description in Pokemon Z. So yes, the Grunts have a reason to follow Lysandre, for they share and follow his dream of a more beautiful world, even though I highly doubt they are aware of the outcome that will occur (AKA No more pokemon)
If you're going to look at Team Flare as the same kind of constructed villain syndicate like that of Team Rocket or Team Galactic, of course they're going to come off as silly. But of course, that's not the case as the ideals behind their structure as a villain team is drastically different from said other groups. In short...they were Team Aqua/Magma done RIGHT, as they had a real outlook on the world that is, in its sense, very similar to what can be said as an outlook on our own world, not warped dreams of disrupting balance.