What you need is a study so put that at front of MR. YeS MR needs doors.
I’d change kitchen a little to make island. You don’t need walkin pantry jest normal cupboards there. Move sink closer..
Change en-suite so entry is off hall not main bedroom.

Is there a reason why you have no living areas facing north, and the garage is on the north side. Are you in Australia?
If in Australia, the morning sun will fill the kitchen and living areas, but by noon the living areas will not have any direct sunlight, winter will be dark and cold in those areas.

Regarding the MPR, the plan is showing doors already, they look like they are cavity sliding doors. Leave as is.

The answers to your specific questions depend on your particular needs. How many bedrooms do you need? Do you need sound proofing or privacy for the media/family room? If you think it is too big why are you paying more for space you seem to have no purpose for?

In answer to what can be done to improve the plan, for efficiency and future proofing you should make much better use of your orientation. As Dreamer said, why are you not using north?

Should I flip the house orientation then so that the garage is on the right side. that would make the living areas be on the north side and would be nice to have the swimming pool on the left side of the house too.

Can you post a plan showing house on the lot with north point and house flipped

I’d convert the space of Bed 2, it’s bathroom and the powder into the media room. Move bed 2 up with 3 and 4, and make 3 & 4 a bit larger and more usable (they are a bit tight).

So where are you? Question is because climate and latitude is relevant. But short answer is yes, northern windows and north facing outdoor areas have important practical benefits.

This is the site plan. Not sure as well where to put the HSTP, swimming pool, and Ruble pit

I also need to put a 12x12 shed later on

I’m building in Queensland, Australia

Yes, flip the house, you have a massive piece of land, so orientation is not restricted and should be a priority.

So cooling rather than heating is a priority?

Any input on the specific questions? It's to suit you, not a generalisation.

I’d be trying to get all the bedrooms on the south side with cross ventilation where you can. Deep verandahs north and west sides at least

my suggestions include a separate study and the kids' lounge and reversing the garage allows the northern aspect for living areas (with a gable end and raked ceiling?) and better location for kitchen, nook and master suite... i've included deep verandahs and the alfresco and, depending on the size of the pool that you want, a narrow pool in the courtyard would make a feature that would also help cool the house and, coincidentally, the shape of the building and the roof with deep verandahs and the bump outs with awning suggests a modern country Australian style ideal for a hot climate

and the location of sewerage absorption trenches will need to be decided by an engineer and can be done when you organise the usual soil samples needed for building applications and it would be worthwhile to include plans for your proposed big shed and the pool in the plans (even if you don't want to add them immediately) as it will more cost effective for drawing the plans and council applications to do it all at once and also better to design the extras to enhance your views and a big rectangular shed could be more efficient to build and use than a 12 x 12 shed

This is a very nice plan oklouise. I should get my builder to look at this. Yes I’ll have to speak with the engineer to draw plans for the shed and pool. Thanks so much