However, it has some disadvantages.1) it does not encourage investors to invest in intangible assets, such as education, training, R&D. etc Many of the developed countries and high ranking companies (AMAZON and APPLE)  invest heavily in R&D.

What, if any, are the disadvantages to NOT having checkbook control?

Are there any disadvantages and/or penalties to buying/fixing and flipping in MD, in a relatively short timeframe?  

Are there huge advantages and disadvantages?

I would use online resources only to become familiar with the benefits and disadvantages of setting a LLC so you can become informed.

I know there are many disadvantages like unpredictable budget breakers, but is there a reason someone would choose a historic home specifically?

IMO, disclosure requirements do not put you at a disadvantage (I spin it as a positive verses "weekend wholesalers").If you both want the option to represent retail sales then you'd both need a license. 

I'm in the military as well and, although I'm only starting out with real estate investing, I'd be more than willing to provide you with some of my insights from the perspective of being in the military and some of the advantages and disadvantages that it affords.

Disadvantages I see: Obviously more issues to juggle building a brand new house. 

We always make offers in the name of the LLC (I've never seen any disadvantage to doing this).As for commission, we'll always find a way to give something to the listing agent (and most of the REO listing agents know us these days, so they know that).