Mindboards

RCX 1.0, RCX 1.5, and RCX 2.0 all used the same mindstorms brick (RCX), although they did differ slightly (and by that I mean that the 1.0 set had an RCX with a power jack).
NXT 1.0 and NXT 2.0 both use the same NXT brick (while it is true that at some point there was a slight internal change, both NXTs are functionally and cosmetically identical).
EV3 is a totally new and a different brick. Calling it an NXT would be like calling an iPhone a laptop, just because both can use the same headphones.

The "3" in EV3 comes from it being the third Mindstorms generation, not the third NXT generation

IMO it's simply a marketing expression to make it sell without any claim to deeper "true" meaning.
Probably the marketing devision really starts counting at Mindstorms RCX (1), NXT (2), and now EV"3" (3).

But actually it's generation something in between 6 to 12 if you take into account the predecessors

Lego PC Interface
Lego Technic Control Center
Data Control Lab
Code Pilot
Cybermaster
Scout
Microscout
Spybotics
RCX
NXT
EV"3"

I don't think lego considers any of the previous systems to be "Mindstorms", at least not like they do the RCX, NXT, and EV3. As far as I know, RCX was the first stand-alone system that you could fully program using the computer, and then set loose to run on it's own. Even if the RCX wasn't technically the first Mindstorms system (and EV3 the third), I completely understand and accept the name.

Both Scout ("Robotics Discovery System", RDS, programmable by the Scout-SDK and/or NQC) and Cybermaster ( programmable by BricxCC and NQC) (and with the SDK, also the Microscout, IIRC) - :
all could be programmed for an autonomous mode, too.

But as I already mentioned -
to me it's only a marketing decision without deeper meaning regardless if it's called "Mindstorms" or not.