1) Would you rather have some extra ships left behind during an attack, or a bunch of colony ships, constructors (costs as much as a cap, if you haven't got entrenchment), and other misc ships getting nuked because they joined by default?
Sins succeeds because by default the various ship options are set to something SAFE, not something good for every situation.
2) Haven't noticed this myself, if it's true that's pretty unfortunate. Have you tried setting the rally point to different things, like for instance the fleet icon in the empire tree, or the icon above the flagship? Sorry if I'm being redundant, it's hard to tell how much experience a person at random has with the game.
PERSONALLY, I would not want single, lone ships traveling on their way to "the front" as they are built - I would much rather give them a rally point in relatively safe territory, then move them all as a group. You could very easily forget about the position of your flagship/fleet and have your ships running, one at a time, through enemy or contested space.
Try setting a rally at a planet near their intended destination, it's really a better idea in the long run. Lone ships flying around... that'll bite you in the ass one day.
3) Again, I'm not 100% sure about this one. I don't play Sins (or any other games for that matter) very often, although I play it more often than most of my other stuff. Anyways, I recall situations where I told ships to retreat from a battle, as you said, and then they immediately jumped back intoo the fight - because they naturally are supposed to be part of the fleet. Perhaps in the intervening time it was tweaked so they permanently left the fleet. IMHO that works better anyway.
Having them leave the fleet is a much better alternative than having them return to a battle with 1/4 of their HP left. Also, I believe you can set units to control groups (ctrl+1, etc) and these shouldn't be affected by what fleet they're in. I almost exclusviely use control groups or else select one of the "pip bars" (left side of planet when zomed out) when I want all the units in a given system to move together.
You can select the pip bars from multiple planets (as in your example, ships which retreated from battle) and give them all a common destination as well.
Finally there's one other thing you could try - there's an automatic "retreat from battle" button in the commands menu, and it probably has a hotkey. When you activate this, the ship will jump to the nearest friendly planet - this way you don't need to take your focus off the battle at all, even to tell it where you want your ships to retreat TO. It's a really cool feature actually... and perhaps doing this won't cause them to be removed from the fleet either - I don't know tbh.
4) I've never played a game with info described in the way you're saying. How exactly do you tell whether they're a noob or an ace regardless? You'd have to ask them, right? So why not look for games titled things like "veteran game" versus things like "noob game, learning" etc... maybe the problem is people not being descriptive enough in their game titles, rather than the game itself.
...Besides which, total game time means nothing about a player's actual skill level, nor does their self-description of how good they are. Someone might say they're experts.... but not mention they've only played against the AI.
