Currently another faction at peace / cold war can:

1) enter a system

2) declare war

3) immediately invade with ground forces ignoring a defending fleet(s)

My expectation is that a defending fleet should intercept them.

This issue is compounded in these scenarios:

1) playing as pacifist where I just want to defend and not gain militarist faction for having to attack a fleet that is attacking the ground

2) playing as the Vodyani with a massive space station that gets destroyed because of two turns of ground battle without engaging the ark

You can actually "ignore" the invasion by minimizing the ground battle notification, kill the attacking fleet, then do the ground defense against the now 0 enemy troops. Ideally, you shouldn't be able invade when there are enemy fleets, but I think they are using this system in order to prevent a similar cheesy strat that was common in Endless Legend (If systems couldn't be invaded when enemy ships were present, the defender could split an inferior fleet into multiple fleets and completely prevent an invasion despite being unable to mount a defense and buying a disproportionate amount of time. This is because fleets can only attack enemy fleets once per turn).

Maybe the ground invasion notification could be modified, where you had an extra option to "mount orbital defense" that throws you straight into the space battle.

Being able to bypass the Ark's defenses into a ground assault seems pretty broken, they should probably have special rules.

I like SirBagel's idea of having an Orbital Defense option that allows for ships to protect a system.  Either that, or limit the number of "Guarding" fleets to 1, and add the rule that you have to defeat guarding fleet before mounting a ground assault.

The fact you can initiate ground battles when there are some ally ships in orbit is silly by itself. You shouldn't be allowed to do that unless having researched a special skill allowing you to sneak and bypass defenses or as playing a faction with a special trait. 

If I had to guess, this is largely an artifact of how ES1 handled invasions, where an invasion consisted of having siege ships in orbit bombarding the planet, which meant that system defense consisted almost entirely of the fleets in orbit. ES2 doesn't seem to have considered the possibility of the system 'end around.'

And can somebody help me out with how the ground combat system works - what's really the difference between infiltrate and blitz? It seems like infiltrate is supposed to make the invasion take more turns but preserve the manpower, while blitz is the opposite, but this is guesswork and not really grounded in the tooltips, unless I'm being somewhat illiterate.

I do not per see think it is a bad idea that you can invade planets in systems with defence fleets. 

However if it is the case there should be more invasion options to pick between, with some of the more brutal with orbital bombardment being unavailable. 

In general there should be a penalty to the invader, or like it was suggested the troop count of the shits in orbit gets added to the defense stack. And the defender gets extra defense options.