I don't think it's the Infinity engine that has a legacy but the isometric CRPGs (and probably the games BioWare made back then). Actually I've started playing isometric RPGS made with the Aurora and Electron engines (NWN games), and only played Infinity games much later, after isometric games were made popular again with PoE, DOS, Pathfinder and so on.
An engine is only a support for developers to make the graphics and the UI. Not sure why the IE shouldn't cope with D&D 3E except by dropping parts of the ruleset, by the way. I suspect it's more a problem of how badly the code was written and hard to modify; BioWare admitted as much themselves.