the Elite AT-AT surely is powerful. It sounds funny, but the Juggernaut is (in the numbers) even more effective against shields but has less range.
There are base designs that deal better with the eAT-AT (Joes). When the eAT-AT began to fire at the shields edge and to crunch walls many rebel bases began to adapt. Walls are much less important now. They're mostly scattered to limit the deployment zones. Rather successful base designs often split the base and shield generators in 3 parts. Put them in three corners and maybe put some turrets also the middle (without SG).
Another base design (see here: http://i.imgur.com/82qHtM6.png
) is more concentrated. It is called BoS after the name of a player which used it with success and showed it to the disney playdom forum.
I use that design currently. I sometimes win, when the SC is filled with Skiffs. And I win a bit more when the droideka is also up. Winning to often is too costly on resources so I'm ok like it is currently.
Skiffs in the SC are a bit vulnerable to air strikes but 4 of them bring an eAT-AT down quite quickly. Often faster than the attacker can use VT-49 Decimators or a droideka on them. Even if it has some repair droids attached.
A Juggernaut (i.e. + sniper) in the SC is much more robust. But one Juggernaut can't bring down an eAT-AT if multiple repair droids are attached. (Or it takes very long.)