well, boys and girls all play together, competing as equals on the same playing field. Then you end up with fastest overall, fastest boy and fastest girl. Fastest fatty, fastest ginner, fastest in the 25-35 age bracket, how ever many way you want to categorise it can be done just from one single race instead of umpteen different groups run over several different courses.
Look at the stat's you will soon see why the women and men are separated in many event's, it's not because women are perceived as lesser, the women and men's events are separate to give all athlete's the opportunity to shine.
Quick example of where dividing men and women is a good thing, seeding a match sprint event via a qualifying flying 200m TT, at this level you would essentially have a result sheet consisting of two blocks of competitors, men and women with a clear divide (baring the occasional exception), according to times posted (women are typically about 0.5 to 1 second down on the men's times). This would then have all of the 1st stage matches being a man vs a woman (slowest vs fastest, second slowest vs second fastest etc etc) and you basically see all females eliminated from the competition in the 1st stage proper, leaving the women to be rated based on flying laps rather than actual match sprint ability. Similarly in other events.
The argument for varying distances between men and women's events etc varies from event to event. It could depend on physiological differences or it could be as simple as something like there being more men involved in the sport than women, thus it being easier to find a team of certain size with men or vice versa (bare in mind many nations don't have such a large pool of athlete's so you would end up excluding certain nations in some cases by forcing equal distances). The team pursuit for example, men ride with 4 riders, over 4 km, women, 3 riders over 3km. 1km per rider on the front (if you divide workload equally which isn't really the case but never mind). Plus there is the money side of things, why combine events and get it over with quicker, when you can drag it out and make more money from tickets?