I just wanted to post some thoughts here that I've been thinking on for a while and below is my comment that came about from a post on Fritz's blog.
I've played a lot of Apocalypse and even the Spearhead mission that allows for super heavies. It's not really super heavies that are a problem, it's the destroyer weapons. While they used to outclass everything else (basically giving you no reason to choose anything other than a destroyer) because of the older blast template rules and the vehicle damage table. Clipping corners of vehicles with large destroyer templates would still hit at full force on a vehicle, usually crippling it or destroying it outright, while the rest of the template also hit another target. Cobras D-Cannons and other 10" blasts will destroy entire vehicle squadrons in one shot.
One further thought on blast template clipping. This is actually the reason why the twin-linked pulsar on the Scorpion is so good, because you can re-roll the scatter to optimize how you clip the vehicles with the double 5" destroyer templates so you can spread the hits over as many vehicles/infantry as possible. Sometimes scatter is good!
6th Edition has changed this somewhat; a combination of the blast rules, and how the damage chart works since it was updated on Forgeworld's site have made some of the other weaponry more appealing though: http://www.forgeworld.co.uk/Downloads/Product/PDF/a/apoc6thupdate.pdf I have had a discussion about this on my last Apocalypse battle report, which you can read over here: https://www.youtube.com/watch?v=Ptcs8dWdVEU
In all honesty though, an unsupported super heavy is basically just going to get evaporated if you are prepared to fight one. They survive not because of structure points and special rules, but because they are hard to get close to. They're hard to get close to because in Apocalypse the table should basically be the most hellish rush hour imaginable with infantry and vehicles everywhere.
The only thing that I would caution is the Imperial Titans, if they explode they can literally remove everything on a standard sized table.