A lot of the battery chargers made in last 20 years or more check the polarity of the battery before turning on the charge current which means you cannot connect charge leads the wrong way, this also has the benefit of making them short circuit proof if you touch the clips together. Unfortunately this means if your battery has discharged below a certain voltage the modern chargers will not charge it, sometimes you have to connect a decent battery in parallel with flat one for a while and charge them both until the bad battery has enough voltage to 'fool' the charger. Modern car batteries are smaller because 'they can be' - modern fuel injected engines start so much easier under all conditions than the older carbed ones that car makers have decided to save some weight and space. The only car in the last 30 years that has suffered a flat battery was my wifes Fiat Punto ( definitely the most troublesome car we ever experienced, glad to see the back of it - was replaced by her first Jazz GD ) because you could leave the radio on with the key out and the car locked.....
You may have to re-teach auto windows, The ECU may have had its memory reset but it will soon re-teach itself - do you know how old the battery is ? It may be time for a new one anyway, modern batteries can last over 5 years, but it is a gamble - they lose capacity slowly over their life and sometimes it goes unnoticed until the battery is stressed.