The philosophical concerns, at least, are easy to express: in a world that's getting increasingly more connected, it makes more sense to embrace that rather than to resist it. Leaving the EU moves in the opposite direction, then, to the way things are developing. Also I think the "time we took control of our own affairs" argument is somewhat bogus. From any individual's democratic perspective the net effect of leaving the EU would be to increase the level of your voice from about 1 in 500 million adults (ie practically insignificant) to about 1 in 50 million (ie still practically insignificant). The UK parliament might gain more control, but I would have no greater influence over it (not to mention my opinion that it's not nearly representative enough, so that arguably I have even less infleunce than in the (roughly) proportionally elected EU Parliament).
Practically I think it's a lot more nuanced, and I can certainly appreciate that if you don't buy the above philosophy then the current practical benefits of the EU are not enough to justify remaining a member. There is a certain amount of self-interest in the decision, too. While my own funding is from a UK institution, many of my scientific colleagues are part of collaborations that depend in whole or in part on EU funding and EU projects (or, indeed, are EU citizens). At least in the short term, these would certainly be heavily disrupted on leaving the EU. It's probably in everyone's interest to preserve these as much as possible come what may, but the point is that certainly such collaboration is easier as a member of the EU than not. The freedom of movement is a benefit, too, as the central experiments are often not based in the UK, requiring people to hop over there regularly (even though the UK isn't a part of Schengen, travel to the EU is still fairly easy currently, and that relative freedom would be at least uncertain if we left).
There's more to it than scientific self-interest and debatable philosophy, to be sure. But, as I said, the practical concerns are more nuanced -- the recent response to the migration crisis has been worse than useless, as I'm sure I've said before. I'd argue, though, that this is because the EU isn't enough of a Union, rather than because it's too much of one. Countries had an annoying habit of reverting to national interests rather than co-operating to resolve the issue. It's been quite painful to watch, certainly.
There are other things I have in mind, but I'm trying not to ramble on too long this time -- particularly because, as I say, if you don't buy the philosophy then I don't think the benefits are enough to persuade anyone to remain. From my point of view, the EU is a) the right direction in an increasingly global world, and b) useful in various practical ways, but I don't think it would be fatal or catastrophic to leave it, at least not in the long-term.