My fanfiction's main plot you can say is a war between the regions with Kanto and Jhoto being allys due to the fact that they are connected against Hoenn and Sinnoh who are also allied.
I am most likely going to incorporate real-life things in this story as well, mostly weapons and equipment. For example solders with XM8's and F-22A's. Now here is a list of some ideas, some of them I have thought of for a long time and some I made on the spot.
Due to geographical reasons, I find it hard to believe Hoenn and Sinnoh could be allied. They are on the opposite ends of "Japan" also in canon: Hoenn is a very warm region whereas Sinnoh is partially covered with snow most of the year. So, maybe Hoenn should be in alliance with Johto and Sinnoh with Kanto, as geographically that would make more sense. Also, the war would be easier, seeigh as Kanto and Johto are connected.
As for using modern weapons, that's really up to you. Personally I would try to go with Pokémon-powered equipment for added interest, but I guess guns do the trick too. You just have to think things carefully trough.
1) Prof.Birch is an armor developer for the Hoenn military and is a leads new technologies for the Military. When he learns of the impending invasion of Hoenn, He gives 3 of his 4 prototype armor suits to his son and two of his friends (Brendan/May/Wally) -This idea I have thought about alot and so I have alot of detail for this one, if you want more just ask-
You know, I really can't imagine Prof. Birch as an armor developer. I mean, as a Pokémon researcher, he's essentially a biologist. Unless those armors are organic and based on Pokémon, I really don't see how Prof. Birch could be working on them.
Also, how old are his son and the other people? Are they in the army? Because if they are young or not a part of the army otherwise, giving the prototypes to them makes no sense. If they, however, are in the frontline of the Hoenn defense, then it makes sense. But obviously Prof. Birch should give the prototypes to the people that can be of the most use with them. Essentially, that would be the army's special troups or whoever are in the frontline of the defense.
2) All characters with strong bonds with their pokemon will be able to speak to each other (pokespeak I belive?) Is this a good idea?
Depends. If they can speak with clear English sentences, then it might be a tad sue-ish. If they can communicate, but not necessarily with English, then it sounds more plausible to me. Or, well, maybe they can have some kind of translator devices or something. I don't know. I only ever use Psychic type Pokémon as translators to allow my characters to communicate with their other Pokémon.
3) The viewpoint of the story will change throughout with many characters, not just the characters in Hoenn. I will change between them and some of my own original characters and characters in Sinnoh (Lucas/Dawn/Barry)
Sounds good, but you have to be careful to do it well. Also, don't use too many characters like that, because it can be very confusing for the reader. You could maybe pick four or five characters whose POV you use and then switch between them when needed. Also, please don't write "Lucas's POV" when you switch to his point of view. You can use his name as a title if you want to make it clear who's talking...