I'm going to make internal layouts (and add them to post #2). Those will answer most your questions in time.
I would go with just ONE capture point, located at the top of the base, behind the Air Pad room, vulnerable to Gal Drops.
A V-Pad in the bottom of the base.
And Spawn Rooms in between.
Sound familiar?
The reason is I want only one CC, is so that resecure attempts are able to focus on one point, it is clear to both defender and attacker what the key points to take are and defense be able to focus with a single instant-resecure strikes on a pressure point or stealth attempt when outnumbered. I want the ticker-tug-of-war system removed completely as it puts unrealistic demands on most defense parties.
I want players to be able to dig in, but I also want a NTU silo, so that bases can be drained in siege (any damage to the base should drain its NTU). I'm thinking of putting it near the lobby bunker. You know, where all the silos are now and that half circle structure. I'm thinking of having to fill three separate silos to get the base fully charged, making NTU runs just that bit more demanding to both attacker and defender (having several silos allows easier access to one, but also means you have to get all back in your control and losing one silo to the defenders so they can refill it only lengthens the siege a little bit, not endlessly like in PS1).
Compared to the PS1 Tech Plant, which had 5 entry points total (Backdoor, Lobby entrance, 2 airpad entrances, Vpad) for the PS2 Tech Plant, I'm going with 6 + vpad shields on ground floor, 6 entry points on walkway level which can be reached by Jetpacks and Gal Drops (2 at the leg-towers leading to the lobby, 2 to the keep) and 4 entry points on the Airpad (2 top level, 2 on airpad level). The SOI antenna and platform will be a separate section that can only be reached from the airpad level, making it ideal for Gal Drops to start at. That building will have 4 entry points too.
That makes for a total of 12 regular entry points and 2 vpad entry points. It is possible some of these entry points (for example the leg-tower points and airpad top section entry points) will have shields which could be deactivated from the inside by infiltrators.
In terms of complication btw:
I want there to be main routes (which would likely be the type of campy indoor fights we know from PS1), with by-pass routes that go inside -> external -> inside. Typically, I want it to be linear or semi-linear fights internally. I see the layout as a line between v-pad and airpad, with CC, gens and spawns as intermediate stages to (by-)pass, depending from which direction you're coming in. I want the spawns to be able to block someone working their way up, or working their way down by taking control of Keep entry points and stairwells. But it will be less complicated since you will only have a couple ways to go, but they also converge again before you take the next stage.
For instance, if you acquire the Lobby and want to get to somewhere upstairs you could fight for the V-Pad to reach the inner keep:
Lobby <---> V-Pad <---> V-Pad Shield Gen <---> Walkway levels (internal) <---> Generator level <---> Spawnroom level <---> CC level <---> Airpad
, but you could also take the longer route:
Lobby <---> Leg-Tower <---> Walkways (external) <---> Walkways (internal) <---> etc.
Which means you would have to fight back into the inside of the keep even if you already had the lobby, it just makes it easier to get to the next line of defense and force the fight there.
But as you can see, you just go around the V-Pad and V-Pad Shield Gen. You still have to get through the upper inner level of defenses to get to say the CC. So you as a defender or attacker, have this constant tug-of-war inside/outside in the infantry only zones and transition zonees. Internal objectives should be reasonably well protected due to defenders always passing by them on their way anywhere and that's a good thing, since taking these points can deliver blows to a defense or defense line. Gaining access to bypasses allows you to cut-off defender routes and push them back a line of defense as well. But in principle, any route the attackers take should put them through a route that defenders take anyway.