Reasons for Thune:
He is a self-described evangelical Christian, and it's stuff like this that provides a sense of Biblical balance to social conservatives who get the heebie-jeebies about Mitt's Magical Underwear.
He followed through on his promise to not serve more than three terms in the House, which holds sway with the limited government types in the GOP.
He scalped Tom Daschle, which raised his profile among all Republicans.
He shares Romney's viewpoints about Iran and Afghanistan.
He never met a social program he liked, and his selection would be the spoonful of sugar the Tea Party needs to make the Romney medicine go down.
Reasons for Ayotte:
She was one of the first to get on his bandwagon.
She, like Jindal and Rubio, represents the face of "diversity" in the GOP. But behind that thin veneer of modern appearances, Ayotte resigned her office of Attorney General when New Hampshire's governor signed three same-sex marriage bills into law. Troglodytic stuff like that makes her a darling who stands on her principles, misguided as they are, to the GOP electorate.
She is anti union (hell, anti worker), pro Second Amendment, anti Single Payer, pro Bush tax cuts, and shares many of Mitt's stances on financial regulation, government spending, and other issues.
Conventional wisdom dictates you pick a running mate who comes from a state with a high number of electoral votes and/or who provides a geographic balance to the ticket. But in recent history, the Republican nominee has picked a running mate who acts as the olive branch to unify disaffected elements in the party or shields the standard-bearer from his weaknesses. A Thune or Ayotte selection would both serve well in these capacities and energize the base. Ayotte would give the party the same initial spark as Palin provided in 2008, but Thune is the probably the running mate the money party would get fully behind over the longer haul.
I could be wrong, but I called Palin as the 2008 VP choice almost six months before it happened:
http://www.democraticunderground.com/discuss/duboard.php?az=show_mesg&forum=132&topic_id=5292974&mesg_id=5293622