could we get some retrofit mechanic/

 currently defender can just wait and see what the attacker has and equip whatever is needed to gain upper hand over attacker, mid/late game

I am inclined to call that defender's prerogative. They've got their ships at their shipyards and they can do a rapid refit if resources allow. 

If you don't like it, then I would suggest not attacking with a min/maxed fleet, instead use something a bit more sensible and less easy to counter.

but wouldnt it be more sensible that defneder needs at least 1 turn to retrofit.currently its too flexible imo

I don't see any reason why retrofiting shouldn't be part of the defender home-field advantage. 

The ship customization is a process where the player has direct means to interact. While I like how it is working now, it could be nice to create general templates @ship designs (energy weapon focus heavy, mixed loadouts, etcpp). This would speed things up a bit. 

I'm against a complete mechanic which would streamline and dumb it down completely. It's a fun part to gather little pieces of information about your opponent and act accordingly. 

Are they using energy weapons? What about their distances and defences? 

It's a nice game to play and reminds me of prominent examples in wars fought were technical advancement was an important factor (think Germans vs. Russins in WW2 when it comes to tanks or general battle tactics).