First time playing this game, and it seems it is already over by turn 3 despite all my heroes and allies are in good shape, trying to play with the default leadership deck with a total of 5 willpower, 3 turns in and the staging area has locations for 5+ willpower, and there's an active location I was unable to explore, am I stuck? (allies have 0 willpower)

If yes, I am surprised this major flaw hasn't been addressed yet and I'll come up with a quick rule to make the game progress such as add 1 progress token on the active location if I commit all my heroes to the quest each turn just to unstuck me or something like that. Thoughts?

Shall I just wait for allies with willpower if there even are any?

I'm not sure what you're doing but it sounds wrong. Have you watched the tutorial videos that FFG has on youtube?

I got a situation where I couldn't place any resource token because my staging area was overwhelmed by locations (with a threat level higher than all my heroes combined) which I couldn't travel to, in order to reduce the threat, because there already was an active location, which I couldn't place tokens on because of the above situation.

Basically I had 5 willpower in total, threat level in staging area was 5+ so no progress token, there was an active location with 3 tokens required which I couldn't place, basically I was stuck, no way to clear the active location in order to move to the next one and try to clear threat from the staging area.

People call this "location lock" and it does happen. There are cards that can help by placing progress tokens on locations in the staging area, like Northern Tracker .

If you are using the 'starter decks' provided in the Core Set, that's part of the problem. Those things are not well designed and don't do much to teach new players how to build decks that can overcome the game's challenges. Unfortunate state of the Core Set, but overcoming that initial challenge was part of the fun for a lot of us I recommend building your own deck by combining two spheres of influence... Maybe check out some of the deckbuilding articles over at Tales from the Cards as well.

Thanks for the answer! I managed to win that match thanks to a lucky +2 willpower stone!

Read this, it has deck building information that will help you power through the scenarios: http://hallofbeorn.wordpress.com/beorns-path/

Location lock is a classic new player problem that can be dealt by knowning when to mulligan and how to customize your deck. I beat the starter quests be using a combination of spirit and leadership. Some spirit is necessary for the solo player. You could also try playing 2 handed (that is play two decks like a multi player game but both controlled by you), which is generally easier.