Difficulties with cleat pedals

I feel fastest with clipless pedals. But you are not alone. http://www.pinkbike.com/news/Which-Muscles-are-Really-Used-During-the-Pedal-Stroke-2012.html

I prefer to ride with older style strap in pedals because I like to walk normally when I get somewhere.

Also your shoes may not be adjusted to your pedals properly.

For how often did you ride during this month? You describe quite novice errors. I've done the switch recently and I understand what you mean, but each time I was scared to do something with cleats or fell, I beared in mind the thought that I simply need to get used to them. Now I prefer cleats to flats, even I don't feel that 100% confident with them. Anyway, the reason for muscle pain is that you use another muscles now. Difficulty to get a quick start is only in your head, moreover cleats let you give exploding amount of power without being scary that your feet will spin too fast and you'll lose the pedals. Same thing about power. IMO you simply don't trust 'em, so I think you should give them another try (for two months at least, if you ride twice a week), and only then you will be able to get some kind of objective conclusions.

Firstly the "uncomfortable feeling in my knees" needs to be addressed and are a concern. You don't say how much and how long your rides are, but its warning that should not be ignored, more so if your rides are short (under about 2 hours).

What cadence are you riding at. With knee discomfort and being used to pedals in the middle of the feet, my guess is you are 'mushing' (slow pedal rate) rather than spinning. You cadence should site around 80RPM - typically faster for experienced roadies and slower for off road MTB. If its under about 60, it can cause knee pain. SPDs work better with higher cadence, so if you are mushing, there is unlikely to be much benefit. If you are a musher, it feels wrong to spin, but you need to for efficiency and your knees. the best thing to do is get out, hit a lower than normal gear and sit in it. Use your riding companions for a guide, ask them what they think - would/are they be in the same gear as you?

If you are not mushing, or you start to spin faster and the knees don't come right, then the cleats are setup wrong. If you think they are right, try changing the angles a little and see if the knees come right. Be cautious, and look after those knees.

In the end, flats are fine if you want to stick them. There is no law that says you have to use clip-less pedals, and not everyone benefits from them. If someone looks down on you because of flats, best option if you cannot ignore them is give them a lot of time to study your rear end on next ride.....

In my experience, my knee pain was always fixed by sliding forward the seat (this kind of alignment). In general, I would check your setup with someone experienced and reliable because there might be a lot of variables involved in this kind of aches.

I think most of the problems you're having are due to being used to pedaling with the arch of the foot. Your calves are weak and get to burn in such a way that you can't push with all the power of your thighs and buttocks, or at least it would make your ankles bend. I can't think of any other reason why clipless pedals would make you weaker, because they make you use more muscles so at least you should achieve the same power.

I see some comments that suggest that pedaling with the arch of the foot is not that bad. Well, for mountain biking it is, because with ankles and calves you absorb the higher frequency (i.e. smaller) bumps, because of their shorter levers I guess. I feel much less in control if staying on the pedal with the arch of the foot, just because of that. OTOH, the "regular" position will make your calves burn until they're not trained, above all in descent, but at least in my case, it was pretty satisfying seeing them growing before my eyes! (obviously the training should be progressive to avoid inflammation of tendons and muscles).

tl;dr

Train you calves and get used to pedaling the "regular" way.