Charging is always going to be slightly odd in any system where people move according to an initiative pass rather than all at once.
You've missed a couple of things in your analysis:
So let's say I am starting out of charge range, I have to spend 2 AP to get into charge range, another 1 AP for the charge to make contact and then have only 1 AP left to attack. Probably not enough to make an attack at all, right?
Melee attacks have a variable AP cost. You can put in as many as you like. Including the minimum of 1. Now the limiter of only spending 1 AP is that you may limit the number of hits you get. If you have a melee weapon with a RoF of 1 or higher you're fine to attack. If you don't, then yes, you cannot attack with only 1AP. Most of the melee weapons have a RoF that varies according to a characteristic (e.g. S for swords, WS for chainswords). So most characters that would willingly charge into melee would be able to attack, though less skilled melee fighters may not be able to use a charge for an advantage from extreme range.
I get the impression from your phrasing that you regard this as a bug, but I see no intrinsic reason for that this is necessarily a minus rather than just a way things work. You either charge from close by or you know what you're doing. An unskilled fighter running 12m to attack someone maybe shouldn't get an advantage from that. At any rate, it is what it is. So long as you're not attacking from extreme range though, or if you're using an easier weapon like a knife, you can charge someone.
Then let's say I am already in charge range and move in (1 AP) and then make my attack. The enemy then spends 1 AP on Evade (if left) and on his turn he can strike back with full AP? If so, this is not good.
Actually, no. Firstly Evade uses an AP so for your charge move (cost 1 AP), they spend for Evade (1 AP), so this isn't a net loss for the charger. In any case, a charge costs 1 AP and a melee attack can cost 1 AP, so the AP-impact is the same whether you attack with a charge or without. The only difference is that with a straight Melee Attack option, you can choose to spend more AP if you wish.
Here's the reason for the anomaly: as the 2 combatants make contact in pseudo-reality both have the same time left within those 5 seconds for attacking the other (ignoring weapon reach). The system doesnt seem to account for that. The charger needs to spend the time charging but the person charged can spend all the time on the charger, causing the mismodeling.
I'm not sure what you mean by the above, but I assume it's following on from the misunderstanding above about AP costs.
At any rate, there can be a significant advantage to charging. It can give a significant damage bonus. In my test combat comparison between DH1 and DH2 (elsewhere), a Maletant charged the party assassin and due to the additional damage bonus, all but took her out of the fight in one hit from perfect health. (Shattered her leg leaving her crippled and prone). Without the bonus, she would have been temporarily down, but able to rejoin the fight.
And the bonus increases with movement rate. I can't wait to see a Harlequinn charging. Then again, they would have a higher RoF probably so it would be an interesting tactical decision.
In any case, the net result of charging is that if you're very skilled, it might be more sensible to take a more cautious approach (relying on your higher RoF), but less skilled might favour the high damage, as would the highly skilled when facing particularly tough opponents they were struggling to damage. I quite enjoy these sorts of tactical trade-offs, personally.