The devs/designers don't understand the strategy of their own game, and anyone who says otherwise is either trolling or is just ignorant of the facts....
Take for example when pbhead actually played a game with a dev...halfway through the game, the dev decided "Well, I guess I better get trade up now"....FACEPALM...and then we have Ironclad devs make statements on the forum about how they honestly do not believe jumping SBs is in any way OP....see things from the designer's perspective? Seriously? They don't HAVE a perspective, because they don't understand their own game....
I can't speak for Ironclad, but Stardock has a history of awful game balance...it isn't what they care about, it just isn't...they want to make cool games that are fun, moddable, and cool...balance is an afterthought...
Now, that in and of itself isn't bad...SD makes great games that for SP or casual MP are pretty damn fun....they have the right combination of good graphics and low performance compatibility so everyone can enjoy the game...and they support modding far more than most games ever could be....but, from a competitive MP perspective they epically fail, and in no small part because no one on their team is even remotely close to the level of ICO players...
It is blatantly obvious that the devs wanted this game to be a titans/caps game, understandable since late game fleets completely wiped caps like they were toilet paper....the uncapped AoEs of titans marginalize frigates, forcing players to focus on titans, caps, and key support ships (which presumably is what the devs wanted)...what the devs struggle to understand is the power of bomber spam, which has completely replaced the "en mass frigate spam" that marginalized caps in the first place during the late game...so, the devs didn't get the titans/cap game they probably wanted because bomber spam still results in the same effect: you go through caps like toilet paper...
The game is sins of a titan, not so much because titans are invincible but because everything revolves around titans now...it's all about getting your titan, protecting your titan, leveling your titan, making sure you don't feed the other titan, finding ways to kill the other titan, etc. etc....cap choices, technology picks, and fleet compositions revolve around titans (which at high levels are damn near impossible to kill without massive massive fleet advantage or...that's right...your own high level titan)....
As far as specific balance issues, they come in two flavors...you have the things like Starbase Mobilization and SttC, which are (or at least were) grossly unbalanced...the devs can't understand how these things are too powerful because they don't understand what eco players are capable of and they don't understand that a Tier 8 lab requirement is a small obstacle for a skilled player...then you have things like Wail which are not necessarily OP but are implemented in very questionable ways and cover up the otherwise weak assets of a faction...
To answer your question more directly, Twilight, the balance issues people are bringing up aren't really because they aren't skilled....it's because either they are truly unbalanced or they just don't like the implementation....jumping orkies is not a "you aren't skilled enough to counter" them....they are grossly OP, and anyone who says otherwise is either a troll or needs to play a game on ICO...wail and titans are implemented in a way that just irks players...sure, we all know how to counter them, but it's not an inability to counter that irks us: some of us simply don't like their implemenation....