Assault Grenades are weak and available on one unit of one doctrine, bundle grenades are good but expensive and no better than a guard grenade, flame pios are glass cannons, I already mentioned rifle 'nades inability to do shit against fortifications. You have to go all out to dislodge this trench, change up your build order, spend big where you would have saved.
Or, you could just waltz up with your basic infantry and toss a retreat button at the defending squad in the trench. Guarantee by the time they evacuate, they don't be in fighting condition anymore.
Reading posts like yours it makes me wonder how germans are able to clear a building before they can use stuka dive bomb or LE.f.h arty.
Also I've got this feeling that you expect germans to have something between KV-2 and KV-8 at around 3-5 minute, preferably as a stock unit.
If you can't use proper counters, then sorry, that does not mean they don't exist or yuo can diminish them.