I don't see that you are playing wrong. Everything you've mentioned seems to be fine. You can't reassign feats in between games. Once you've chosen them, you've chosen them. (Or at least once you've played with your choice. If you chose a skill feat at the end of the last scenario and the following week before playing the very next scenario said you wanted to change your mind, I'd let you.) And if you add a character, there are rules for replacing a character in the middle of the adventure path. Just follow them:
If your character dies, start a new character for the next scenario. Choose a character card (it can be the same character who just died, though you do not get any of the feats that character previously earned) and build a new character deck as described in Build Your Character on page 4, choosing only cards with the Basic trait. If your party has begun the adventure The Hook Mountain Massacre, you may ignore the Basic trait restriction; instead, you may use any cards in the box from the base set and the Character Add-On Deck, as well as any cards from an adventure deck whose adventure deck number is at least 2 lower than that of the adventure you’re currently playing.
So the new character shouldn't have any skill, card, or power feats and should follow those deck construction guidelines. Lots of people have chosen to ignore that and if you look through the forums, you'll find ideas for alternatives. If I was adding a new player to the game (and we were far enough in that catching them up by replaying didn't seem feasible), I'd probably let them take all the feats for the group. If it wasn't to far into the adventure path, I'd meet with them outside of the group time to catch them up by playing just the two of us.
I play as a group of 6 and we grant the feat rewards to the a player that can't attend a night of game time. Of course, their cards didn't improve, so they didn't get all the benefits we did. (Plus they missed out on the fun! Which is penalty enough.) We recently did that when one of the guys in our group had to leave for the summer to work at NASA. There was another guy that had wanted to play, so he's our sixth player now. We were at the end of Burnt Offerings, so we just let him pick a character, gave him all the feat rewards up to that point, mostly a basic deck, but let him scavenge a few cards from the former player's deck.
I do think ensuring 90% success on checks is a bit high. I like to definitely be above 50% and probably end up being around 60% to 70%. One of the things to remember about damage, there are other ways to take damage besides failing a check to defeat a monster. There is Before the Encounter, After the Encounter, location effects, barriers, even some boons deal damage. In a lot of those cases, those armors and damage reduction powers are going to be helpful.
For me, I'm not trying to necessarily optimize my characters. I'm trying to make them fun for me to play. The power feat or skill feat I take may not be the most powerful, but if it lets me do the thing I have fun doing, I'm taking it. That is my preferred approach to the game. Same thing for my party composition. I encourage everyone to just pick a character they'd have fun playing. I don't care if it means we end up playing Valeros, Amiri and Seelah. Or Merisiel, Sajan, and Harsk. I wholeheartedly believe we can still be successful and we'll have fun doing it.
As far as number of characters, and this is only personal opinion, I would say 3 characters is the minimum I like to play with. 4+ is what I find most enjoyable (and 6 is a whole different world of fun). But obviously, you can't always do that. When I play with just my wife, we each play 2 characters to give us 4 total. If I played as a group of 3 players, I'd maybe consider playing 2 each. When I play just myself, I play 3 characters (though I'm thinking of trying a duo of Amiri + Lem), just because 4+ was too much for me to manage solo.
So, if your group is 3 players, I think you are fine. You might like it a bit more if you could find a 4th player, but 3 is still fun.
Most of that is opinion, but the one thing that is closest to non-opinion is "have fun." Make sure you enjoy playing. I'm pretty sure that is what everyone who puts any effort into contributing to this game wants, for you to have fun. Whether they be a designer, publisher, editor, playtester, or forum community members who spend entirely too much time thinking about PACG and creating turntables, storage boxes, worksheets, location stands, layouts, etc, they all want you to have the same fun they are having.
Good luck on your adventure.
I think Hawk has some great points, but I wanted to comment as well. I think the key with the game is to have fun. It is a game after all. Mike and Vic have said as much as well. That is one of the big reasons for letting people create their own banes, boons, character, whatever.
I don't think that you really need to ensure success on the rolls. Sure 90% is nice, but my group plays it a little risky. We don't do a lot of scouting, and we just go headlong into a lot of encounters. For us cooperating is the biggest thing. To that end, my groups play with their hands showing. This way, you can tell who might be able to help you, and exactly how much help you might get. This helps you decide if you can press on or if you should just end your turn.
Armor is considered on of the weakest card types in the game right now by most people, but I think that there are definitely case where is can be useful. As Hawk mentioned, armor helps you with more than just combat. Also, to my previous point, I think that armor lets you be a little more careless with you explorations.
When group size is considered, I actually prefer 3-4 people. I have a group with 6, and while there is a good amount of talking with other players, there is also a lot of downtime between turns, and I think the most fun is in taking your turn, and making decisions.
More on party composition, while the number is a concern, for my group, the types of characters is of more concern. As I said, we play a little more recklessly, so we NEED a divine character with a heal. It is an unfortunate side effect of our all out play style. Now, in a more conservative group, that might not be the case. in my group, we are currently playing a new comp, which doesn't have a healer, and we are finding that we are much more cautious and don't try to get boons that aren't directly related to our character, since it is tough to use cards to get boons that you are going to give away. In essence, don't let the team comp concern you so much when you pick, but let your choices influence your play style.
Meri is great with items, but you can really build a character any way you want to build it. If you want to try a recharging Theif build, then go for it. Also, how you build your character will be a reflection of your comp and group. For instance, in my 2 person group with Meri and Lem, both are very suited for combat, since both need to be able to kill things to get into the location decks. But in my 6 person group, our Lem is designed as a support character, with Aid, Find Traps, and the like. Just feel it out and find those things that work.
When it comes down to it, just have fun and do what works for you. The game is such that you will lose some times, but you learn from it, and will get better as you go.