Yes, I would like to keep battles on a small to moderate scale too - not sure where the other developers stand on this, but that's my preference! Fleets of 100 dreadnoughts are just silly... If you need 100 of 'em to make a fleet, they're not really dreadnoughts, are they? :P
With that in mind, I think we'll be going for a mechanic where you can design a ship of any arbitrary size, so if your opponent has 100 so-called "dreadnoughts" in his fleet, there's nothing stopping you from upping the ante with a fleet of ten super-dreadnoughts!
We are definitely learning from SE5... the game is completely 2D (apart from perhaps some parallax scrolling backgrounds, but hey, they had those in the Sega Genesis days!), and when we get to implementing a ship design screen, we are NOT going to use slots - just lists of components like SE3 or SE4! So adding 100 of the same component would probably be as simple as picking a component, clicking "add", and adjusting the quantity installed!
Not sure what exactly you mean by "user defined variables", but we are using a reasonably sane scripting language, namely IronPython. Right now the galaxy generation is done by a script, so it would be very simple to adjust in any way! Also, it's looking like achievements (e.g. technology) will be at least partly script-based, so I imagine that would fit in to your "space monster" scenario - instead of an achievement which triggers when you reach 100 research accumulated in Physics and causes you to gain Physics Tech Level 1, have an "achievement" which triggers when your ship enters the forbidden nebula, and causes a bunch of monsters to spawn!
Speaking of tech, we've got some interesting ideas on how to do research... think of "research points" and "engineering points", where the former is used to discover new techs, and the latter is used to improve old techs (though you might be able to funnel your RP into engineering if you really want to improve that one old tech!) RP would be produced primarily by research labs, but EP would be produced by building and maintaining things. So you build a laser cannon, that might earn you 5 EP toward lasers, and each turn your laser remains in working condition, you gain another 1 EP toward lasers. Then these EP might be spent toward new laser prototypes (say, a laser with 20% more damage). if you have RP, though, you can spend them toward laser theory (which would reduce the EP cost of any future laser prototypes). This last part isn't quite so certain yet, but if it works the way I'm hoping, you'll be able to create new laser components up to a certain level (say, 2 attributes improved by 1 level each, or 1 attribute improved 2 levels) cheaper than investing in laser theory, but if you want the really fancy stuff, it would be more economical (assuming you have RP to spare) to invest in theory first before building the prototype! (Keep in mind this tech stuff is still up in the air at the moment - I just thought I'd post it here to see what folks think before we go down any particular path with it!)
So yes, that does mean you could potentially create your own variants of components in-game... create a laser with +2 on the damage slider and call it a High Energy Laser, create a laser with +2 on miniaturization and -2 on damage and call it a Point Defense Laser
I hope this doesn't seem too confusing... that's part of the reason for the Engineering Points being required to create new variants - it's not just for realism, but also for keeping a player's choices on the ship design screen within reason! If you could create new variants of components for every single ship design willy-nilly, then that would make ship design take FOREVER!