The battletomes can seem like an upgrade, but really they are more or less balanced with grand alliance options. Take Khorne for example; mono-Khorne armies just got a lot better with their new battletome but that's because previously a 'Khorne' army was just a Chaos one that limited itself for no mechanical gain. Khorne-themed armies utilizing warp lightning cannons and Sayl don't really gain a net power increase because the benefits of Khorne allegiance from the battletome come at the cost of loosing the WLC/Sayl.
But this is perhaps most obvious with the recent Kharadron release. The Kharadron allegiance abilities are flat-out awesome, generally better than other battletomes. But limiting an army to just Kharadron units means losing access to a huge number of options that are huge for a normal army. Kharadron really have no troops for simply holding the line, extremely limited mortal wound access, no spells or prayers, no cheap chaff options, and only one choice for battleline. But that's why they get such sweet allegiance abilities.
So where does this leave you? That's a bit more tricky. Because is you play Tzeentch allegiance and win the other player may blame your allegiance even if that was not a significant factor. What you are going to want to do for preventing the perception of anything being OP is limit one-sidedness of battles as much as possible. This means you'll need to keep an eye out for cheese builds, make sure the scenarios used don't overtly favor certain armies, and if you really want to be safe you'll need to eliminate random initiative as well. But above all I would say to keep open communication with all players so you know what people are liking/not liking.
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