If you want to get something realistic, go play Kerbal Space Program.
Let me throw in some stuff too:
1: Given Shivan expertise in subspace technology, this is plausible. While Shivans can definitely do subspace things that have impact on gameplay (precise jumps, possibly disabling subspace drives/comms), there are some other things. Like Blue Planet's description of Sathanas claiming that it removes the unimaginable amounts of heat generated by these large beams in front by radiating all that energy into subspace. Or using completely unstable jump nodes.
I think a simple way to force Capella to go nova (wait, wasn't that a multiple star system?) would be to just open a huge subspace portal inside it, directed to somewhere, and either suck out matter from its core or force more matter to flow through that portal into Capella (just have the other end of that portal inside a denser star). This method to throw a star off balance is rather simple. By the way, ever watched Stargate SG-1?
2: While there was a mention of whether any light-speed communication with Sol would be disclosed or not or if that investment in post-war GTA (with Shivans, HoL, GTI defectors and completely wrecked economy) would be even possible, in Freespace we do not have a magical immediate FTL communication anywhere we want.
Look at that
. From this you can see that a vessel's subspace drive needs to be in a gravitational field (of a solar system) in order to even work properly and trying to make a jump to a location far into outer parts of a system seems to require a) a lot of power to stabilise a subspace corridor, b) computational abilities to predict an optimal path of some sort in an unstable subspace field.
My guess is that subspace normally is very, very energetic and unstable, but gravitational fields close to their source are able to fairly well stabilise local parts of subspace, and vessels using a jump drive as we see in FS are able to only move in such subspace environment, probably because in a more violent areas a ship travelling in FTL would have been just vaporised or forced to use excessive amounts of energy to prevent that from happening. (Note: Jump nodes seem to be temporary natural "corridors" of stabilised subspace between "bubbles" that are solar systems) So if we imagine FTL comms being basically a tiny subspace corridor between comm systems of two vessels into which radio waves are sent and received on the other side (again: Stargate), even if you would somehow manage to open a corridor between Sol and Alpha Centauri (energy requirements!), any objects sent would probably be vaporised and any message sent would be either too corrupt to be even registered as a message or completely indistinguishable from the subspace background noise.
Also note that tightly packed star clusters could have really complex subspace mechanics like dozens of jump nodes or most of the space inside that cluster being accessable with a basic in-system jump drive.
Freespace ship speeds seem to be relative. I think it was mentioned in some campaign that your speed is measured relatively to a close notable revelant object, like a space station, huge warship or an asteroid. I suppose that would also mean these objects are the center of mass for a gravitational system like, in example, planetoid-you or capship-you-others.
3: Either nav systems of Bei's wingmen malfunctioned... Or 10ly isn't actually that much off the scale in this case. See, in reality N362 is a star cluster, not a single neutron star. As I mentioned earlier, star clusters could have really complex subspace dynamics and the presence of a massive neutron star probably isn't helping too. I guess that in such a system 10ly is a realistically achieveable distance of an in-system subspace jump with that huge navigational error being caused by multiple interactions of that cluster.
4: That war is intergalactic (in more detail: between our galaxy and a stray star cluster outside it IIRC), so the distance isn't that ridiculous, but it doesn't matter either way since the only way to get to another solar system is via a jump node and the same seems to be true between galaxies/star clusters. And I think it's settled that travel through a jump node is really fast.
The other issue is a sense of scale: if the Ancients are that arrogant and have similarities with humans in that domain... Well, our definition of "colonised" is "some people live there", not "we are fully utilising the resources of a whole planet". If you ever watched certain videos of Isaac Arthur on Youtube, you would probably know that our whole solar system is able to provide us with stuff to build a civilisation with a fleet exceeding most things seen in science fiction by several orders of magnitude. Even better, Jupiter and its moon system are also able to do it. For example, look at UEF in Blue Planet: Sol has got a similarily sized population and economy to whole GTVA. Or Mass Effect - the known civilisation spans the entire galaxy, but only a fraction of a percent of stars and systems are accesible to travelers. In ME the effective range of travel is: mass relay systems + very limited FTL range. In FS it is: wherever a stable jump node decides to form and only the insides of that solar system. So it's very probable that Ancients had only a couple dozens of systems colonised and Shivans could even originate from that single system and build an enormous fleet only with resources available there. Heck, you can hide fleets as huge as moons or planets in such a single solar system. Noone's looking there anyway.
So that battle is important in two ways: in a way Ancients think it is - honour, pride ("we've never lost a system") and in a way a little bit more serious - to hold them off in that place because otherwise they will break into your territory and slaughter everything (just like GTVA's defence of Gamma Draconis and later Capella).
5: The story is about races noticing each other when they have similar tech levels, because if that isn't the case... there's no story. Just an immediate slaughter or subordination. Also, what will a single high-tech weapon do for you when your enemy has got millions of more primitive guns?
Not to mention that multiple races with similar technology advancement arising in a short period of time is a quite possible situation when there is something like the Reapers.
The thing making this situation (humanity vs Shivans) a lot different than a simple comparison of military forces is intelligence: since we're intelligent we know how to use stuff like viral weapons in order to even take control over enemy assets. This isn't actually a case against Shivans, but I think you get it. In Blue Planet's case the problem is whether Shivans want to kill humanity off or if they need that not to happen at all.
Yes, humans can kill Shivans, but infinity minus one is still infinity.
Also I've always thought that Command is actually stationary somewhere in fleet HQ and all the info and orders are sent through a system of subspace transmitters and relays through jump nodes to the desired system where Allied units are located. That would need a device sitting near a jump node in the nebula and transmitting stuff, and I really doubt GTVA would attempt to expand into that nebula without basic comm infrastructure.
How many ants does it take to kill a human in an F-16? How many F-16s can humanity field? I rest my case.
If we assume that an ant has no weapons like a Shivan and also no realistic way of damaging F-16's hull, in order to kill that man they should... a) fly en masse
into fighter's engines until they're completely clogged up, fail and the whole fighter crashes. Yes, flying ants exist. Or walk into the engine when that fighter is stationary on the ground. Or hide in the cockpit instead and just eat the pilot after lift-off.