I don't believe what you're stating will change anything. Some of those were already there in the first game and had little to no effect.
Some were present, yes, but not all.
1) If you attack with underwhelming force, the nearest guardians just converge on you and chase you out. Depending on your goal you might use long or short range, but in general you would avoid this situation except for special tactics (feint, etc).
2) If you attack with roughly equal force, all the guardians gang up and come after you. They might lose, but you'd have a use for either short or long range because you're going to be forced to fight unless you leave the planet entirely.
3) If you attack with overwhelming force, all the guardians group up around the command station and rely on shields and whatnot to wait you out until the SF or SR or whatever arrive to restore this to a #1 or #2 situation. You could use long-range to siege with minimal losses, but if the short-range plasma cannon does 5x as much damage as the long-range plasma torpedo (for example), you're going to have a strong motive to use the short range cannon in order to break the defenders before their relief arrives. If you don't, you'd either have to pull back when the relief arrives, or engage the relief and suffer more attritional losses than an earlier close-range assault would have cost.
4) If you attack with a force so overwhelming that none of the relief forces could get there in time, or couldn't make a difference even if they were all there now, then all the guardians (and their guard ships) retreat into AI territory to join a threatfleet or something else like that which preserves their value. That just leaves some static defenses around the command station (and maybe one other strong static point around a data center or whatever), which you could whittle down with long-range and minimal losses. But if you had that much force you can probably quickly kill what remains regardless of your weaponry.
In situation #4 you might prioritize killing the defenders before they can leave, and you might choose to do that with long-range to minimize your losses. But, again, if the short or medium range weapons are sufficiently more powerful than the long-range weapons, it might make the difference between killing 25% of the defenders before their escape, and killing 75% of them. You'd have to work out positioning, shield placement, etc, so you could catch the defenders, but either way you'd also need the heavier weapons to get the job done.
To summarize: there are situations like assault and pursuit where the long-range weapons
would not achieve the objective due to running out of time.
Even if the AI is more responsive, kiting & outranging will beat everything else because outnumbered + outgunned means the best strategy is to shoot without being shot.
That assumes that the defenders are either stationary or too slow to catch you in a reasonable period of time. In classic the guard posts anchored down most of the normal defenders, and player speed was buffed so much relative to AI speed that you could often kite indefinitely. In the sequel most of the normal defenders will be fully mobile, and the AI defenders will be able to catch you unless you're only using fast units (which excludes the stuff with long-range siege capability).
Sorry, but that's a bad justification. It's not because it's simplified compared to a complex mess no one even dare to try understand that it's simple enough.
Relative simplicity isn't the point, correct. So I'll restate: each weapon will be good against one of four target types. How hard is it to know which one you need more of, and to know which of your tools provide it?
Does it make any difference if some of those tools are variants (modular) instead of entirely different ship types?
I should add that my goal here isn't to deflect your criticism. Deflection is easy, but does nothing to improve the game. I just think you're wrong.