A lot of people seem to think in extremes when thinking how seasons would effect the game. If it is winter the region won't just instantly be covered in snow with christmas lights all around it. You won't be trudging through the snow everywhere and skating across where all the water used to be. Here's my two cents:
Seasons will have aesthetic changes in some parts of the world but not all. Now obviously having snow or tumbling leaves in the middle of the desert would make no sense. If it snows in winter, it'll effect the north most part of the world (assuming Isshu is in the northern hemisphere) and the area surrounding the mountains in Isshu. It won't snow everywhere. Seasons will most likely change the commoness of pokemon in certain areas, it'll effect the play expierience but not limit it, which is likely nintendo's motto with seasons.
Simple pokemon like Pidgey for example though, would stay the same all year round. However Spearow may all be part of a large flock and travel to a different quadrant of the region for each season.
The bug pokemon may have preferred periods when they like to be out. Caterpie might love the Spring, but be uncommon in Autmn and Winter. Weedle might love Autumn but is rarer in Spring and Winter. They both love the summer and thrieve in it, but they both go in decline during the Winter.
The oceans are filled with Seakings, Mantines, Sharpedos, Seadras and Lumineon during the summer time. But winter brings a shift in the climate and these pokemon become more uncommon. They are replaced by pokemon the thrieve in cooler waters such as Dewgong, Cloyster and Sealeo, these pokemon are also available in the summer but are far less common and prefer to stick to icey grottos in northern waters. The summer pokemon mostly head south when winter comes, but a few still hang around to be avilable to you.
The forests around the mountains are effected in the winter, a small blanket of snow covers it. Sninubs, Snovers and Sneasels venture down from the mountains to make use to the forest's resources. They are also avilable in the summer but only in the mountains they call home. Furrets and Ursarings have mostly gone into hybernation, but still appear occasionally if disturbs from their slumber. Not all forests are effected however, only the oens around the mountains or to the north.
Grass pokemon shift around the region to meet their needs. Sometimes even approaching forest bordering the desert in the middle of winter in an effort to absorb more sunlight. Most head south though, in summer there is a more even spread out.
Winter isn't all bad though. Ghost pokemon find comfort in areas where a lot of pokemon have left to fight the cold heading for warmer territory or hybernating. The nights are longer, so dark pokemon appear far more often as well as nocternal pokemon. These measures make up for the small decline in variety that i described before.
^ Just my ideas.