Fighting Enemies is Supposed to Be Fun, Not Brutally Difficult
The purpose of enemies throughout the level is basically to let the players use the character’s abilities and powers in creative ways and to provide challenging and/or fun gameplay for players. Fighting enemies is not supposed to be a frustrating or extremely difficult task unless they are a boss or mini-boss they can be more difficult than average, but never frustrating to the point that players want to give up.
There are exceptions to every rule but you will alienate some players by making it super difficult throughout the entire game. Games that boast a high difficulty level are the Ninja Gaiden and Dark Souls series. These games make up for the incredible difficulty with awesome graphics and rewarding gameplay that makes players feel like they accomplished a great feat after every level. Beware of using tactics that artificially increase the difficulty for players, like providing no checkpoints after major battles or having players severely outmatched with no way to defeat an enemy without grueling work.
Enemies Are Meant to Be Fought Not Avoided
For various reasons if you give players a chance some of them will always choose to avoid certain enemies rather than confront them. Many times it’s to conserve health or save time, because an enemy that can be avoided altogether without affecting the main story or level progress isn’t a primary concern. Some players just like to avoid confrontations that seem unnecessary and others want to break the game however possible, sometimes by sneaking by an enemy or using some other tactic to get around them without a fight. It’s your job as a developer to give the players an incentive to take on and defeat every enemy.
Sometimes it’s using cool sound effects and graphics or a catchphrase that plays when players do a great job that encourages interaction, other times players are motivated more by good loot and upgrade opportunities. You should try to make players feel like any small-looking enemy could potentially have a significant challenge / reward and they will be more likely to take a chance and fight to see what they happens or what they get. It never hurts to have the enemies taunt or otherwise annoy the player when they are in range or hearing or eyesight, so the player feels more satisfied by taking on and silencing the offending enemy.