I'm a little late to the party, but here goes.
Players are important for any game, and developers always want to keep retention high. Having that not be on high on their to-do list is a quick way to get to failure town.
The big issues stated by the OP weren't actually brought up by Muse themselves, but by the players. Team scramble, choosing the spawns, weapon and ship balances, etc were all issues players brought up and discussed well before Muse addressed them.
---------------------
That's not to say all the players wanted it, but you'll never get all the players to agree on anything. Depending on what circles you spend your time in, you'll get a different 'general impression' upon what players want. Muse decides to listen to everyone and evaluate their ideas and suggestions. They don't focus on just the hardcore players, or only think about the casual gamers. They look at what support players give ideas, as well as the negative reactions to those ideas.
The spawn system for example was something that was brought up quite some time ago, but was pretty low on their to-do list. Balance tends to be near the top, because that's what makes the game fun and exciting. Speaking of balance, the 'nerfs' to close range weapons was probably well called for. The latest updates weren't really all that detrimental. I think the gatling actually received more of a buff despite the range reduction. So while a lot of the guns were adjusted, they're all still viable.
http://www.cracked.com/video_18537_the-7-deadly-sins-online-gaming.htmlThat video sums up a lot of gaming sins. In particular, #7 Pride brings up what occurred prior to the balance adjustments. Players would find a ship/gun combo that worked alarmingly well, and just stick with it. It's not playing unfair, but that particular build would be so effective, that the only way to beat it in most instances was using the same build as them, only doing it better. This is what would lead certain clans to timing distance and counting bullets on these builds to minimize kill times. Currently a larger variety of builds are viable, making the game more interesting.
Skipping on down to player retention again, you can just view the current steam charts. Being the person that brought these up in the first place while talking about player retention, the first thing I notice is that the rate of player loss has decreased quite a bit compared to most of the player influxes. It's still too soon to see how it will ultimately play out, but you also have to take into account the conditions of the influx. Schools were out for break, the game was on sale, and fans of the youtubers saw them playing it. Now schools are back in session, the game is no longer on sale, and the youtubers aren't focusing on this game. The player count was guaranteed to decrease, but we have yet to see if it bottoms out to the original norms, or if it'll stay a tad higher (or maybe even bounce up a bit).