1. Shinta and Qum are just two children that Char found in Dakar. They were probably homeless or orphaned (or both) which is why Char brought them with him. I don't understand what sense it makes to bring children in a non-emergency situation to a battleship, but that's another story.
2. Without a doubt he was influenced by Macross. After the premiere of Macross in 1982, practically every real robot show out there shoved in a transforming mecha somewhere, either as the hero's mecha or something else. It's even thrown into series that don't have transforming mecha otherwise - Dunbine has the Billbine, and L.Gaim has the L.Gaim Mark II. However, of all the post-Macross 1980s real robot shows, I think Zeta probably had the most transforming mecha, as even ZZ scales back on that a bit as the novelty died off.
3. It's a plot contrivance - she had to escape easily somehow to run back to Scirocco and piss off Katz more.
4. This is explained in Zeta. When you communicate over the radio, the enemy can pick up your transmission and use it to determine your position. However, when mobile suits touch each other, the sound is vibrated throughout the suit's body, making the communication private and untraceable.
5. This is just a fact of Gundam - every villainous organization cranks out lots of mobile suits. Just look at how many suits the Crossbone Vanguard tosses out in a movie like F91. This is something that you'll find in many mecha series- it may make 'sense' to concentrate on a few suit designs, but that translates to less model kits to sell. One of the few exceptions to this rule is Gasaraki, which throughout all its 25 episodes only feature two mecha designs. As for one-of-a-kind suits in Zeta, specifically the Messala, Palace Athene, Bolinoak Sammahn and The O, those are all handmade by Scirocco himself, so they're separate from the regular Titans MS development tree. As for Jerid, I don't think you can say he pilots 'so many' one-of-a-kind suits, as the only one that comes to mind is the Byalant. Everything else he's piloted, there's more than one of.
6. I think at some point the Argama must've acquired a second unit, or they just had LOTS of spare parts. One of them has to be true since Reccoa's unit is totally destroyed by Yazan, yet Fa has one that lasts well into ZZ.
7. Yes, the technologies are radically different. All mobile suits in the Universal Century use nuclear fusion reactors, while non-nuclear Cosmic Era suits use batteries. Now, even though UC suits can operate a long time with their fusion reactors, they can still run out of propellant.
8. I really don't know. I doubt it would be a way to "honor" Zeta - to me an homage consists of a quick and occasional nod to something else, not lifting plot points and dragging them out for half the series.
9. I don't necessarily agree because we don't know the full storage capacity of ships in the SEED universe. For example, after episode 28 of DESTINY, the Archangel is carrying a very large load, including the Freedom, Strike Rouge, Sky Grasper and a bunch of Murasames. And the Minerva is estimated early on to hold at least 10 suits. Why not stock more suits? To make it more dramatic and focus on the main characters. The Minerva had a couple of GuAIZ R pilots early on, but they were killed, placing the focus on Shinn, Rey, Lunamaria and Athrun. Afterward, when it comes time to fight Destroy and Freedom, it's just down to Shinn. It would've made sense if they added at least one grunt pilot to replace Athrun, because by the end of the series, the ship only has three pilots. Even in Zeta when they have large team battles, the focus tends to be on people like Kamille and Char, not the Rick Dias team.