The Kilrathi were tougher to beat than the Nephilim.
Here are my reasons:
1) Against the Kilrathi you typically had just 1 wingman. Against the Nephilim you have several.
2) Nephilim armaments aren't as powerful as the Kilrathi comparatively. Sure the odd bug fighter has the heavy plasma or heavy gorgon, but almost every kat fighter sports enough guns to ruin your day. Meanwhile the bulk of the bug fighters are left with puny masers/quantum disruptors.
3) Damage repair systems seem more effective in 2681. Back in the day, 1 or 2 hits could smash your guns, blow off missiles, shatter your radar or reduce total shield or engine output. In the WC3 era onwards any sustained damage rarely had such negative and permanent results.
4) The Nephilim aren't as aggressive as the Kilrathi. How many times have you flown against Squids, Skates and Stingrays and watched them run away? Do the Drakhai run away?
5) Comparatively speaking Confed fighters are on whole better than their Nephilim equivalents. In WC1/2 the Kilrathi fighters either equalled or surpassed their Confed rivals.
My 2 cents...