Thing about Pokemon conquest your energy determines how strong your Pokemon is. There are 5 levels of energy your Pokemon can have: the weakest is a blue arrow pointing south, weak is an arrow pointing southeast, neutral is an arrow pointing east, strong is an arrow pointing northeast, and strongest is pointing north.
The higher your energy the stronger you are and vise versa.
the ponigirl item also increases your energy if used in battle regular by 1 stage, red ponigirl by 2 stages, blue ponigirl by 3 stages, and and purple ponigirl by 4 stages
Now to answer your question sense raising energy boosts your stats you see that your Pokemon are weaker because of the change of your energy
Some skills allow you to raise your Pokemon's energy is it is below strongest examples:
Father Figure Blocks enemy critical hits and increases Energy for all allied Pokemon. Ujiyasu (Rank II)
Grand Dream Two treasure boxes will appear upon defeating an enemy. Increases Energy (for 3 turns). Hideyoshi (Rank II)
Great Uniter Two treasure boxes will appear upon defeating an enemy. Increases Energy and Attack (for 3 turns). Hideyoshi (Rank III)
Kabuki Dance Raises Energy and Attack of all allied Pokemon. Okuni (Rank II)
The mood maker ability also improves energy by 1 stage but only for the turn for the Pokemon in its range
Hope I helped
Sources http://www.psypokes.com/conquest/skills.php
http://bulbapedia.bulbagarden.net/wiki/List_of_Abilities_in_Pokémon_Conquest
http://bulbapedia.bulbagarden.net/wiki/Ponigiri
And playing conquest a lot
