[2020] New House

I agree that the Dining Room is an awkward location to play on. To clarify, are you suggesting ultimately removing the tiny office or sealing it off at the outer door? Completely removing it would create this awkward space underneath Bathroom upstairs. You still have an additional window in the small office on the right side. I don't really understand how changing the door in office to a window would improve the situation. My suggestions for playing that site would be to either open up the wall in TV Room that is next to Kitchen a bit to give you a line of sight into Dining Room from where they would normally go through if pushing through Office. You could also play on Red Stairs to give you visibility on players pushing that way from the 2nd floor and have line of sight into office. Additionally, you could open up the hatch in Master that is above where the hostage is and keep an eye there. It's not as easy to hold as the other sites it seems.
Can you give any further examples of indefensible access points? I personally think Defenders still have quite a bit of an edge on Attackers on House.
As far as Spawn Peeks go, most of the spots I've found are for the APC Spawn area. The team is looking into possible solutions to tone down the frustration of runouts/spawnpeeks. However, I think the best way currently would be to learn where to expect runouts/spawnpeaks from and be cautious. You can also choose a different spawn location instead.
There are actually four Bomb site locations, not two. This rework was designed with more casual players in mind, which is why the map is not going to be added to Ranked any time soon.

Turn the side office door into another window so they can't just blow up the door and stroll in.

Again, I don't really see how it makes a difference in changing the door to a window. I think it really depends on how the person is pushing through that entry point, but you have more visibility with doorframes, especially since you can see their feet when they are approaching. I suppose there is more commitment when you vault through a window, and it can be hard to fight back sometimes.

The upstairs bedroom has four points where you can just walk in. The door at the back, the door from the bathroom, the door from the boys room and the door from the stairwell. At least two of those need to be removed or turned into areas where the attackers have to vault in.

I assume you are talking about Master Bedroom?

There are three actual doorways, the one from the main stairs, the one from bathroom, and the one from reading room. There is also the closet that is next to Car Bedroom. There is also the two exterior softwalls. I like to run Kapkan since you can put traps on doorframes to slow their push from Bathroom or reading. Additionally, Lesion or Ela is helpful since their gadgets give off audio cues to let you know what direction they are pushing from. You could use Castle to shut off windows in Bathroom or the long hallway. You can stick Deployable shields into the doorways to provide cover and slow attackers down. I think holding the corner with the sofa chair isn't necessarily a bad place to hold. I suppose you could also run a Mira in the bedroom closet to keep an eye on Car room and Reading Room so they can't push through closet. Reading room would also be a good place to hold to look for anyone pushing from that direction. You could also sit in Bathroom as well.

The girls room, same deal. You can walk in from the door at the stairs, walk in through the new hallway, walk in from the side door leading to the mezzanine. Five defenders isn't enough to cover all the ways they can snipe in, shoot in, spam in, and just stroll in.

Pink Room you can open up the wall in the closet to provide a rotation hole. Reinforce the outside wall of the closet and the wall closest to the stairs. You could hold behind the sofa to watch an angle into the hallway by spiral stairs. Long hallways can be covered by the back corner. You can use Melusi in that hallway, as well as barbed wire, Lesion, Ela, put a Frost trap under the window at the end of the hallway. There are several different options to cover long hallway in various ways.

In adding the new hallways and corridors, it feels like the other rooms were made smaller, turning them into spam rooms which the attackers can just flood with flashbangs.

Defenders have Jager, Wamai, and Warden to counter Flashbangs. I typically play a lot of Wamai to help prevent abundant use of utility, since that seems to be a popular tactic.

Unless you know in advance which operators the attackers are choosing, it's impossible for the defenders to pick any operators that can reliably fend off the attacking team.

That is the entire point of the game. It is the same thing for Attackers. You don't know who the Defenders are going to pick up until the Drone Phase. You just have to have an understanding of typical team compositions. In my opinion, you should have someone like Jager to eliminate throwable utility, someone to counter hard breachers like Mute or Kaid, someone to roam and provide intel like Cav or Ela, someone to provide support like Rook or Doc, and someone to hold anchor on-site like Kapkan. You should be making sure all your bases are covered.
An example would be Doc, Bandit, Valk, Jager/Wamai, or Smoke/Maestro. Doc can provide support for the whole team by healing. Bandit counters hard breachers. Valk can provide intel. Jager/Wamai can counter nades. Smoke can help push people away from pushing a certain direction. Maestro can help delete utility and provide more intel.