Scenarios have a fixed starting race. If you want to play as another race, you would need to create a copy of the scenario with that race set as starting race.

Also, the scenarios were created for DL and haven't been updated for DA and, more importantly, TotA, so there will be bugs in them.

You have to use the Scenario Editor for this. The 'GC2ScenarioEditor.exe' is located under 'Galactic Civilizations II - Ultimate Edition\Twilight\Tools'. There are faster ways to get there (like the game launcher), but I don't know if they are available with the Steam-version.

In any case, you need to load the file 'Battle of the Gods.gc2scenario'. You can find it under ' Galactic Civilizations II - Ultimate Edition\Data\English\Scenarios'. Now, change the 'Player Race' to the one you want to play. You should also change the 'Scenario Title' slightly. Otherwise, you might confuse it with the original. Once that is done, save it via the 'Save as' option and give it a different name.

Still, this doesn't fix the bugs. Primarily, that you don't start with all the techs, because they didn't exist in DL, and that the Thalan are not available as an enemy. To fix the latter, go to the 'Teams' tab, and click on the box in front of the 'Thalan' entry to enable them. To fix the former, go to the 'Technologies' tab and click on 'Terrans'. Then, click on the first tech under 'Available Techs', scroll down to the bottom, and shift+click the last tech (this should select all the techs). Now, click on the 'Add' button in front of the 'Starting Techs' box, and then on 'OK'. Once that is done, do the same for all the other races.

Is there a way to make the AI build capital ships (if you give them all the techs) instead of those dinky little fighters they like so much?