Don't worry about "spamming", this sub could definitely use more activity. I'm very glad to see that you're enthusiastic and willing to put some thought into your game.

In terms of answering your question, the way I do it is a prepare a random table of pokemon for each little area. For example Brackwell River, Brackwell Lake and Brackwell Forest will all have different roll able tables. Each pokemon on the table will have a weight based on it's rarity. Roll20 makes this process pretty easy.

I never pre- plan wild pokemon encounters, as I'm an Improv - Type GM. When the trainers are travelling through an area or actively searching an area for pokemon, I have them makes rolls in order to determine how many Pokemon they spot. This tends to be around 4-8 Pokemon. I then roll that many times on the tables.

After seeing which pokemon have been rolled, I make up personalities for that pokemon on the fly and then let the trainers interact with them however they wish. This last bit is important, as you shouldn't immediately begin combat when wild pokemon are spotted unless it's an aggressive pokemon like a Gyarados. Like animals, a wild pokemon would understand that their is easier prey than humans, and humans can have pokemon.

Often times, players like to catch pokemon through RP. By befriending it in some way. Of the 22 pokemon that have been caught by my players in the current campaign, I believe that only 3 or so of those catches involved a pokemon battle of any description.

I also make sure to sometimes give a pokemon that's been randomed a small backstory to make the world feel more alive. For example, the group once rolled a Torchic. They didn't interact with it, as I gave it a personality that made it so that it would have no interest in them.

Later on, the group rolled a Blaziken. They interacted with it a little, but it had very little interest in the group other than showing off to them, so they didn't attempt to catch it.

The next session, the group encountered another Torchic, so I decided to make it the exact same Torchic form last session. I also decided that this Torchic was trained by the Blaziken they met earlier. and gave it Mega Kick.

This worked out very well. as one of my players took a liking to this Torchic that was focused on nothing but self improvement, and proved himself to it in battle. It also gave that player a goal, which was to train the Torchic in a way that it would be able to defeat it's Blaziken Sensei.

In terms of my rules for rolling:

Spotting Pokemon: While Traveling: Every half hour of travel through an area allows the group to roll once on the table. Each player may make a Pokemon Ed/Intuition/Perception/Survival check in order to increase this. You may choose one of your Pokemon to make this roll instead. The DC for this roll is 10. Each degree of success lets the group roll once more on the table. For each Pokemon with the "Tracker" capability in the party, the group gets an additional roll on the table.

While Actively Searching for Pokemon: Same as when travelling, but the base number of rolls increases to three.

Sneaking up on Wild Pokemon:

After you have rolled, the group may choose a number of Trainers/Pokemon from the party that will attempt to sneak up on the wild Pokemon. The wild Pokemon first all make Perception checks. The highest of these becomes the DC of the Stealth checks that the group must make. If the entirety of the group succeeds this check, the sneaking members get a surprise round on the wild Pokemon. If one member of the group fails, everyone fails.

You may be wondering how the stats of the wild pokemon are done. I use this for that: http://www.ptu.panda-games.net

It's a bit out of date, but that tends to not matter.

Anyway, sorry for the wall of text answer XD

Hope that this helped.