What are some house rules to improve Pokémon Master Trainer?
In my circle we have played that game numerous times. 

Some things that worked for us to adjust the 'strategy' of the game are:


EXP and LVL: if you have a lot of D6 lying around ( I buy them 18 at a time from our local dollar store) you can use them to track level on your pokemon. Then each time a pokemon wins more battles than they currently are in level you can roll the die up. Each level adds 1 to their power. We did this to try and balance the fact that it was fairly impossible to beat an elite four battle without having two +5 item cards.
Allow random battles: Instead of capturing being the only option when you land, allow the pokemon to fight. You roll two dice for the 'wild' pokemon and you can fight as usual. If the pokemon is 'defeated' you can place a marker on it. This marker acts as a permanent + or - 1 to catch. This adds a level of strategy because it may make more sense in the red area to try and defeat rather than catch first, however you better be sure you can get back to that square before someone comes in and snatches it up.
Allow rolls to 'ace': If a D6 is rolled in battle and rolls a six it can be rolled again. This helped again get around the fact that you needed +5 items to beat the final battle. 


Now these things don't necessarily affect the strategy of the game, but it does lead to a more entertaining game and it does give incentives to use more than one pokemon. We found ourselves using the mystery dungeon or 'evolved combo' pokemon only and that was not fun. The level up system lets you use pokemon that are weak through to the end of the game. 

The trade cards though 'horrible and mean' serve a very important purpose. They keep one person with a set of beastly pokemon from ruling the game. Without it you can easily get one person with three of the four mystery dungeon pokemon and that is more unfair than having one snatched from you.