The largest offenders, from which hardpoints were removed, are the Oxide, La Malinche and perhaps the St Ives Blues.
The Oxide had two additional missile hardpoints removed, from 6 to 4. It was apparently deemed too powerful (2.5 damage streak Era?), even with the lack of JJs.
Ignore the slightly broken textures:

Edit: A different, newer picture, complete with ALSO broken cockpit:

Damn...how do I Blender? At least I learned how to go full resolution...all my old ones were at 50%.
Even with 6 hardpoints, unless it's using Streaks or SRM2s, there just isn't the tonnage to have decent ammo while boating 4's. Still, no reason to not have the hardpoints available. The other jenners have 5 and 6 available, all while having access to JJs. This is a completely ammo dependant, ground-ridden Jenner.
Next is the Banshee. Did you know it might have been intended to be Jump Capable? In the files, clearly labelled "calf_jumpjet" and "center_torso_rear_jumpjet":

With the arrows pointing down.
The La Malinche is certainly one of the worst banshees, having fewer hardpoints in worse positions. Now, a JJ capable mech that can only be optained by money might be of concern, but the variant certainly needs some love.
Last is the Vindicator, although it seems to affect the chassis as a whole. There's a 3rd missile hardpoint modelled, which none are using. In fact, the Hero is the only one that gets more than one. Not sure if the worse variants should get the third, or if all of them should get it. An advantage over BJs, who cannot take any missiles:


As an honourable mention, there's also a Victor chassis that I've never seen before; the 9A.
A Victor with 2 ballistic slots, both with 10+ slots unrestricted.
Stock:

Dakka

Why I think it was restricted:

(Dual Gauss Assault mech, or AC40 back in July 2013)
Now, I haven't looked into all of the chassis, has anyone else heard of other things that were removed or restricted for IS mechs?
Clans still have some very nice ones restricted as well...for pretty good reasons.
Edited by Mcgral18, 10 December 2015 - 04:50 PM.