You mentioned pokemon game, therefore I'll assume you want to include skills for your monsters.
I'd say your main problem would not be stats, but rather skills (as far as I can remember Pokemons ;)). Your problem has a bit different category than, let's say, RTS games face. In most of RTS games units don't usually have skills (or if they do, like in Starcraft, they serve particular situation(s), but not general case) and it's easier to evaluate their overall value* and design stats - even concerning leveling possibilities.
But onto your case. Let's imagine situation in which you possess two different Pokemons A and B (stats described relative to each other):
- pokemon A has less HP, little more attack, little less defense, attack debuff skill;
- pokemon B has more HP, less attack, little more defense, no skills at all
From stats point of view, Pokemon B is more valuable as defensive one. If you design Pokemon B to acquire slightly more defense and HP with each level than Pokemon A does, you can notice how his value increases with each level even further. But, take into consideration how this one attack debuff skill can affect battle result. If this skill's power rises with each level then it becomes less clear which of these two is more valuable in general. Going even further, you can use Pokemon A for weakening opponent's Pokemon-with-powerful-attack-and-powerful-attack-skills, take as much damage as he can handle (assuming Pokemons' skills are restricted in use count) and then use Pokemon B to finish him or even use other offensive Pokemon C. Considering greater effects of one Pokemon type on other Pokemon type - possibilities are endless.
Conclusion is: you should not concentrate purely on Pokemon stats, but on overall mix of fighting/defensive/put-what-you-need-here stats including skills. In your case, skills are probably most vital for gameplay, thus making your task even more difficult. My advice is not to concentrate on balancing stats in early/late game, but make them unique in terms of stats and skills. Diversity is what makes your units more attractive to their owners and serves well the purpose of putting greater challenge to the player.
* value does not mean costs, but overall usefulness of this unit