Short test: This was done in double wild Pokemon battles, with my Reshiram and Zekrom attacking each other
Zekrom: 396 Atk, 234 SDef, vs Reshiram: 399 SAtk, 236 Def. Both Lv.100
Reshiram used Cross Flame (93 damage)
Zekrom used Cross Thunder (203 damage)
Zekrom used Cross Thunder (99 damage)
Reshiram used Cross Flame (209 damage)
Zekrom used Cross Thunder (99 damage)
Reshiram used Cross Flame (189 damage)
***It appears that Cross Thunder / Flame get doubled in power when used after the other.
Cross Thunder or Flame also get boosted at any time they are used after each other. In another match, I had both Zekrom and Reshiram attack the wild Pokemon instead of each other. The one who used the move after got the boost, while the one who went first didn't get the boost