The core of your argument is that Tenchi will end up with Ryoko because they are alike. That's not how one usually chooses their significant other.
Let me say why I think Harem End is True End.
Tenchi's never shown any specific preference to one girl. He's had 'moments' with all of them.
Tenchi's descended from Juraian ancestry (and will very likely hold the Juraian throne someday). As we see from the series, Juraian society is polygamous.
Another related series, Tenchi GXP has an actual harem ending, so we see that TM's creators have no qualms in going that way.
If Tenchi were to become Emperor of Jurai, each of the girls can bring something of worth to the Royal line, Ryoko's dealing with pirates and hax, Mihoshi's connections with the GXP, Ayeka and Sasami's noble blood, Washu's scientific genius and finally Sasami and Washu's divinity.