Vin,
There's no technical or theoretical reason to call a 13' x 16'5" room "too small" for a Home Theater. Mine has a slightly different form factor, but is almost the same size (yes, I know, I live in a city house in Europe

).
Of course a bit more space is always nice, but (to play the devil's advocate a bit here, because we all like our HT to be big) there are also other considerations.
a. Once you're seated in your HT, that bit of more space (to 16' x 18'8") doesn't add THAT much anymore to the overall quality of the room. Especially not from a viewing point-of-view and if you calibrate your HT properly audio-wise, not much in that respect either. The law of diminishing returns.
b. I understand plan 2 will provide you with space for two nice and always very useful closets (one in the bedroom and one in the bathroom) or cabinets. Perhaps even a "build-in" wardrobe for the bedroom.
c. The beam in your HT wouldn't be too much of a (technical or visual) problem, but it's not a nice view either.
d. Granted, the guestroom is just for guests - but are you sure you will never want to let it use in some future by members of the household, e.g. a kid?
e. A properly equipped bedroom will add more to the value of the property than a slightly bigger HT (it's sad, but that's how it is...).
f. You can use some of the space you gain in plan 2 by better sound-proofing the HT, perhaps even to a superior degree. Very important in the direction of a bedroom!
(e. You may win a few inches back by placing the projection screen somewhat closer to the wall.)
So... my heart would say "make the HT as big as possible", but my good sense makes me advise plan 2.
Good luck with your final decision, it will be difficult!
Cees
PS Probably no need to say this, but don't forget to bring a cable and an ethernet connection to the bedroom. If possible and applicable.
C.