NPRs do "cheat" in a few major ways;
1) research doesn't cost them any money, this is because it was found they frequently went bankrupt which crippled their research making them useless in fights.
2) their ships don't use fuel. This is a fairly major issue but it's simplified this way to prevent bugs and more lag which would occur if AIs needed complex fuel logistics.
However AIs don't really exploit this, their engine and ship designs are fairly logical and similar to what players might use, because ships have limitless range they could just choose to use maximum multiplier engines on everything but they don't. You might find your ships are slow because you aren't using sufficient tonnage of engines, or very high multiplier. By ion I usually have ships doing 3000 km/s standard with 20-30 % engine and 1-1.25 multiplier. Fuel use is high but manageable.
It's interesting you mention them staying outside your missile range, I've never seen this happen, maybe that's their own missile range they're holding at?
They definitely don't have perfect intel on your ships as I have consistently slaughtered AI ships with inferior designs using various tactics.
Survey ships tend to get lost in first contact, it happens to everyone but the best way of avoiding it is making surveyors small therefore less detectable, and putting good passive sensors on them. Think size 5-10 thermals on a 4000 ton ship.
Point defence can be tricky, undersized missile sensors are basically useless, you need minimum size 6 detection range of 5 times the speed of the enemy missile. If you're travelling towards the enemy ship you'll need to add 5 times your own speed too. The game should pause once enemy missiles are detected. If you have a good thermal equipped ship in every task group you'll detect missiles before they're even in range of your actives. Automatic defence can be very tricky to set up and I can never remember exactly how to do it on the forum, I'll run through it later when I get in a PC.
Once again aurora should auto pause when you find a new race or hostile contact, unless you're running with minimum increments which causes updates to continue.
Post some of your ship designs, Maybe they could be improved somewhat?