With the exception of Emissary/Cerebros and possibly the sound chip, the differences are cosmetic. And while the TakaraTOMY version may look more aesthetically pleasing to collectors, also consider...
* The TakaraTOMY version comes out four months after the Hasbro one was first released here.
* TakTOM's RRP is significantly dearer. ¥29800≈AU$395≈CA$388, and that's before shipping. Compare this with: AU$370 (CA$365) at Myer, AU$249 (CA$246) at Big W or AU$160 (CA$158) at Premium Collectables. The cost of shipping varies depending on which method, but as a super rough guesstimate, let's say the cost of purchasing a TakaraTOMY Fortress Maximus with shipping to Australia costs $500 in total. Okay, the TakaraTOMY version may be aesthetically nicer, but you may be paying an additional $340 for that privilege. Even if I were living in Japan and paying directly in Japanese Yen without conversion and ordering it on Amazon Japan with free next day delivery (so about $300), I'd still be paying more than Big W's or PC's prices (although it would be cheaper than Myer's).
So while the TakaraTOMY version is nicer, the other thing to consider is value for money. If you think it's worth paying an additional $340 for more G1-accurate colours and a toy-accurate face on Fortress, then go nuts. But for those of us who aren't that fussed, then we can enjoy saving that money (which we would likely spend on more toys).