Breakthroughs in safety and containment led to the "warp core" being installed in the engineering hull and the considerable "slimming" of the nacelles.
Actually, while this is not directly supported by anything we see in the show, I PERSONALLY treat the radical redesign of the power generation system seen in TMP as an outgrowth of the interaction with the First Federation (Balok's people).
I also see the redesigned nacelles to be an outgrowth of the modifications made to the engines of the Enterprise by the Kelvins.
Just like we were explicitly told by Gene Roddenberry in the ST-TMP novelization he wrote (or partially wrote, anyway) that most of the sickbay modifications and advances were brought back by McCoy after his sebatical among the Fabrini.
It makes sense, really... radical changes in technology may not necessarily reflect evolutionary changes as much as radical, revolutionary changes based upon new discoveries. And we KNOW that there were multiple new discoveries during the time of TOS, don't we?