What two words always start a fight?
The initiative mechanic is an industry standard. In its basic form, you roll, they roll. High roll goes first. All things being equal you go first about half the time, they go first about half the time and there is a certain balance achieved. What does initiative mean in the real world?
Actually the give and take of Initiative in game systems is way more forgiving than the real world. A truly experienced combatant could take several actions before less skilled opponents can respond. When the fur ball starts losing that initial momentum cal lead to people going to ground, being defensive and seeking to live, not strike back. Initiative can mean very little in a close up fight, with everyone shooting and striking like mad.
Some tweaks to Initiative follow. Why just use one system for a game? There are many different forms combat can take.
No Initiative. Combat is nasty. You may still roll to see who makes their hit and damage rolls first but all hits and damage take effect after everyone goes. That guy you just cheesed can still blast you before he takes a dirt nap. This mode is great for truly brutal close up fights, like close quarters aboard a boarded vessel. Surprise becomes vital as in most systems it allows a free round of attacks with no fear of reprisals.
High Roll Initiative. You take turns going first based on the roll of a die. This is just to allow some play balance. Damage is assessed immediately. You die before you attack, you don't attack. Again, Surprise is very important. Getting free licks in is always a good thing.
Modified Initiative. Skill, environment and position can affect your initiative. This is fine if you have higher relevant skills or the better position or situation. If you don't, consider investing in some combat bots or cannon fodder NPCs. It does reward taking a combat savvy leader into combat (usually only one character's skills are taken into account).
Individual Initiative. Everyone rolls for their own initiative. This takes longer but is considered more realistic by some. It involves more record keeping as to who goes before who. Simpler systems merely establish whether a character goes before or after the opposition.
Persistent Initiative. Roll for Initiative. If you win, you win it for s number of turns equal to the number you rolled higher than what you needed to succeed. For example: if you roll three higher than your opponents, you keep initiative for three turns. Obviously, this only works with rolling for initiative once for each side. I especially like this for air combat. Whoever attacks first usually gets it right and keeps attacking.
Other effects of Initiative. In the real world mortal combat (as I understand it) Initiative represents taking a more aggressive stance than your enemy. Your gang moves faster, shoots straighter, and shoots more. You get there first, and you bring moar dakka to the party. To represent this perhaps you can give a small bonus to hit for the winners or a small minus for the defenders. You might also represent this by having a side that loses initiative grab cover more and advance slowly, if at all.