-There is the addition of anti-structure cruisers, so if you assault a starbase you can get 2-3 of 'em and kill the starbase quick. They have a larger range than the starbase. If you want to lose half your fleet, go ahead... Also, I haven't tested this, but the Advent progenitor + guardians strategy may work versus a starbase.

-But upgrading said starbase to actually be a threat takes a while (a few minutes at least). In that time you can kill it. There is also a build penalty for building in an enemy system, I think?

-You can spam very weak, instant-400-XP starbases... or you can spend a ton of resources on upgrading one starbase to be a major, major threat.

-There's a starbase ability that prevents the planet from being neutralized.

-Starbases have a 30% hull, 100% AM penalty for anything jumping out of the gravity well. You can avoid it, but it'll just hurt you more. Especially if the enemy had a fleet one or two jumps away...

Personally, I love starbases. Means I can properly stay behind my big walls as the AI attacks the base and my capships steadily get to level 10. Especially around a star with 4 fully-upgraded starbases...

SB's were made for single player and ruined multiplayer - you think of that when enemy vasari player starts building mobile star base on every planet.....

Your overall assessment is pretty true actually. Most games I've played online with Entrenchment end up with everyone having starbases on all their planets and then it ending in a stale mate (someone just gets fed up with the 6 hour game and logs off).

The anti structure ships work well against regular defenses but not so much against starbases. Against TEC and Advent bases they are ok, but against Vasari they are useless, you're better off attacking a Vasari starbase with a bunch of capital ships.

The best option to take out a starbases is bombers, again the vasari star base can move so you have to kite your carriers around, but since the vasari starbase is so powerful at it's full upgrade, it can usually corner the carriers and destroy them. If not, the 14 fighter squads will suppress the bombers enough to drag the conflict on far too long. 

In the beta starbases were much much cheaper and less powerful, which I enjoyed a lot more. I prefer having weaker starbases on mutlipler worlds with a very large range and hangars. This limits raiding if you put in the resources, but doesn't cause a stand still between factions. I did really like that they added the penalty to jumping from a starbase gravity well and the prevention of colonize ability, but with the final firepower of a starbase, it's highly OP.

As a design standpoint though, they are awesome for single player because I can play 8 hour games, amass huge fleets and invade and such. For Multiplayer though they seem to just cause a war of attrition. Where the attrition isn't to the game resources, but more to how long a person can stay online and play.

I don't have a problem with the starbases, I think they make the game a little more interesting.  They are NOT free, so a player who builds one and upgrade it has to sink a lot of $$$ into it.