Most of your concerns isn't caused by the airline but security protocols imposed at international airports worldwide. So its neither NNIC.
Answers:
1.First you must distinguished airports whether domestic or international as additional protocols are imposed on the latter's terminal, ie ICQs. You could have considered those. I guess there were lapses on your part, considering you know better than the rest of the two.
The problem you had is you are domestic going international. Your proposal is not going to happen.
International arriving passengers doesn't have problems transiting the same terminals for international destinations. I have witnessed it myself.
T1 for example, arriving passengers with international transfer are herded to transfer desks located before the passport control. Like all international terminals, they undergo the same security protocols.
Domestic arriving passenger does have a problem with that. What you have witnessed is bay optimization, where domestic aircraft is used for international flight and vice versa.
The thing about bay optimization is airlines have the bay never the gate, meaning it doesn't use the terminal while it disembark passengers. That is the reason you go down the stairs at the side of the tube to be bussed where your designated terminal is. Same thing happens to the cargo on board.
This is not the first time either, as CEB has been doing it at T3 for quite a while now, before the pandemic began.
2. NNIC shuttle departs every 15 minutes. In between, PAL shuttle departs every 15 minutes. So you have 7 minutes if you wished to be shuttled to t2 and 15 minutes for t3. Not bad. If you have shorter connection, you are usually told to take airport taxi instead. That you didn't take. Mistake no.2. 2 hour is very short connection.
3. Not possible. answer at number 1.
4. Not possible. You are asking for a centralize terminal when NAIA is not.
That is possible only on a Terminal by terminal scenario, and unless you are international passenger. Airlines knew where their passengers are coming from. So they wait at the gate for you for your immediate transfer should your flight arrive late. PAL has been doing that at T1. Not for domestic passengers though. Again same answer as number 1.
5. That is not NNIC concern but that of government particularly BI. What is peculiar about our immigration pattern is OFW traffic, where they have separate lanes for further verification of their papers to make sure their deployment is ligitimate.
Even the tourism lane is now invaded by unscrupolous employer abroad, so a thorough check on your departure is required to make you safe.
Can you imagine a tourist going to Siem Riep without a job back home or salary incapable of paying fares and hotels. Much more an empty stamp passport. That instantly register as red notice.
But your concern is ligitimate. For regular traveler, its usually a breeze. I've been using e-gates and its so darn slow unlike in other countries. What they need is for upgraded software for them to work faster.
I hope this brings order to your otherwise stressful journey. Remember, procedures are there for our own safety and convenience. You just broke two of them. And made it. Without the convenience. Sounds fair to me.
Notes: Airlines do wait for you when you're already checked-in and wiggle your way out of immigration. In fact, they are usually there calling your name if you are last one. Most likely than not, you and your company were not the last one. There are still others at the back doing the late check-in as usual. Check-in counter closes 1 hour before departure.
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