I have not played any other weather scenarios than the Gettysburg ones. The play balance can be affected by weather but I have not noticed this yet. The weather should be similar to the actual battle and VP and objective hexes should be taken into consideration.
On another subject VP hexes in my opinion are a guidelines for those that are not familiar with the actual historical battle. In the early days

when I was not familiar with the battles I used the Objectives hexes as a reference to what the commanders at the time felt were important and focused on them counting on the designers to have that in mind. As I grew with the knowledge of the battles and history I eventually realized that the key to victory was the destruction of the enemy army, the objectives were important factors in the overall strategy but as the situation changed, geographical positions and advantages, the enemy Armies destruction was the major and primary important factor. The objectives often became irrelevant to the overall defeat of the enemy.
If the weather affects your ability to achieve the Objectives and VP points without the means to defeat your opponent than the problem is the VP's and objectives not the weather. Don''t discount the weather as a fun and interesting factor because of the objectives VP's . Work it our with you opponent if you can. Concentrate on destroying your opponents Army and you will not worry about objectives they become irrelevant after awhile.
If you defeat the enemy Army you have won regardless of the Objectives and their worth, however the scoring may not reflect this but most of the time it does. Just keep few small units to cover the VP hexes. Keeps marauding enemy units at bay.