So wait, We're going to get punished for chain deploying and we'll have to deploy more ships?
Didn't say that
It won't as alot of the "required" chain/ hero flagshiping happens at the early game when you are out numbered and outgunned.
Hmm. That totally doesn't match my experience. I'm not saying early game is easy - it requires some piloting skill, for sure - but for me the easiest way to progress through it has been to kit out the your ship decently and then add on frigates/destroyers with officers as money allows. I've done it *many* times and have never felt like I had to chain-deploy to win battles. Chain-deploying comes into play as an option when you've got a lot of skills maxed out and several high-quality ships to do this with.
Is it possible that you're basing your assessment on playing with mods, which may change the early game balance? That's the only thing that comes to mind. I'm not trying to discount your experience, but it just so completely doesn't match mine that I suspect something is different.
... those "OP skills" are the only thing that HELPS new/ early game players ...
This is true, but the flipside is that those same skills, when used by enemy officers, make the battlefield much much more dangerous for your allied ships, discouraging you from deploying them as it gets towards the later game. Skills heavily skew offense over defense, so that's just a natural consequence. Any mistake is more deadly, any failure to capitalize on a mistake is more glaring, etc.
-The battle joining needs to be less hidden from the player and less OP on the enemy side while giving more control to the player by allowing them to ask for help while also allowing them to deny help just like the AI can
There's a thread about this in suggestions; I've made a note to add something to the UI to help here.
Basically you are saying that people have to play the way YOU want them to play and not anyway that you feel is "boring or OP"
Nothing is black and white here, but that's basically "game design". It can be heavy-handed or not, it can work or not, but in essense the goal is making the game mechanics/UI/etc such that the players are encouraged to do things that are fun and not encouraged to do things that are boring. Obviously both of these are subjective evaluations. I don't think I'm too far off the mark in wanting to eliminate "kite for over an hour, literally" as being the optimal strategy when faced with a large fleet, though.
Maybe one solution to explore to make the phase ships a little less annoying to fight would be to make their phase upkeep cost rise as their CR goes down. That way their normal state would be in normal space, phasing only to do a maneuver or avoid shots, rather than their "normal" state and popping out of phase only to fire their weapons. In term of UI you could have the same green/red indicator as the shield upkeep in the info card, and you could see it in refit when playing with the CR slider.
Of course that means yet another tweak of the AI...
The issue with that is that "having enough flux to make a firing run" and "not having enough flux to do it" are pretty binary for phase ships. I mean the "run through target, turn around, and shoot it" thing they do. So once phase upkeep went up over that threshold, it'd make phase ships - suddently, and not gradually - change their behavior to "basically useless". Although, really, once their CR starts going down, it's already pretty late in the game in terms of how much time they've got left, so I'm not sure this is addressing the issue at the right time.