Obviously it all comes down to what's most effective from a plot/storyline/gameplay perspective.
If a ship needs to be indestructible, it will be.
If a ship needs to be destroyed, it will be.
But...
But there was only the one Collector ship, and it got destroyed in straight-up combat by a stealth frigate. If anything it appears to be inferior to a regular Alliance Cruiser.
The Collector ship absolutely destroyed the Normandy in the opening scene. Sure, it took a couple shots... But only because the Normandy was so nimble. Instead of just standing still and getting vaporized, Joker had that ship dancing around and trying to dodge shots. Which just prolonged the inevitable. That Collector weapon had absolutely no trouble slicing clean through the Normandy.
I'm not sure what to classify the Normandy II as... Is it still a stealth frigate? It's still got the stealth thing going on, but it's much bigger.
It's got the absolute best that Cerberus can afford, which is apparently quite a bit better than what the Alliance uses. Comments to that effect are made repeatedly. So the new, improved, vastly superior to Alliance technology Normandy II is able to take down a single Collector ship... But it isn't an easy fight. And if you don't upgrade the Normandy II even further you wind up suffering some heavy losses during the fight.
And then there's those laser drone things that attack the Normandy II before you even get to the fight with the Collector ship... They do some serious damage to the Normandy II, and they're very agile. A larger ship, or a fleet, would have a very hard time dealing with a swarm of those.
I don't have a hard time seeing the Collectors giving the Alliance a real run for their money.