It seems odd that when others transplant an Uchiha's eyes, they inherit the abilities of that Uchiha (even in the case of Obito, who is an Uchiha simply lost his original eye). However, in the case of the EMS, it simply acts as a refresher for the sibling's previous MS (and takes on the appearance of a fusion, complete with increased potency).
Am I the only one who found it strange to look into a normal set of eyes of a super-strong shinobi (http://www.mangapanda.com/naruto/620/17). ET-eyes, Naruto's Kurama-eyes, Naruto's sage-eyes, Sharingan (Kakashi, Obito, etc.), MS, EMS, Rinnegan, Byakugan, Guy's white eyes (while he is in Hachimon-Tonkou, third gate/life gate)... It's good to see that normal eyes can be helpful from time to time.
By the way: Does anyone have a good explanation, why Hashirama isn't just immune to Amaterasu (if Madara can use it, what I believe), and perhaps to Tsukyomi (if Madara can use it), but at least to Genjutsu? It was even enough to corner Pain.
Hashirama's immunity is just a guess, however...
Since the Sharingan originates from the Juubi, AND Mokuton can be used to control the Juubi (also it weakens and binds tailed beast which also originate from the Juubi), THEN it's a good guess that Hashirama's Mokuton will also weaken, dissipate, or absorb the Chakra away, from Sharingan techniques like Amaterasu.
Even if it's only a guess, it a pretty logical guess in my opinion.
@lakritze, i never put into question orochimaru's skills. if my post was confusing then apologies. my point was orochimaru intentionally limited the power of hashirama and tobirama when summoned against sarutobi. it would been too dangerous to give them full power in such tight enclosed space. you do not summon "redraw the maps" type of shinobi into a cupbard! oro was ignorant of a few things then, dds for one, but he was no fool. regulating their power in the barrier was smart and who is to say that once he succeeded in defeating sarutobi as he planned, that he could not then boost their power to their natural levels once outside the barrier and in konaha village proper? that's my understanding and opinion. orochimaru had excellent skills, the dds that sealed his arms and the kages was the perfect trump and couldn't have known it.
@paulbee, zetsu's are weak because they lack a clear will to drive their capabilities. will of fire considerably affects leaf ninjas and their power. zetsu's, having no will or nothing and noone to fight for prevents all sorts of developments. i thought about your question many times after seeing the differences in mokuton behavior after obito's flashback. it takes will and motivation and feelings to develop power. strong feelings cause sharingan and the more powerful feelings become the more powerful sharingan becomes, eventually waking ms. strong will is what brought jiraya back from the dead to carry out one last heroic action, allowed ooniki tsuchikage to get back on his feet for a grand dust jutsu and is what got tsunade toe to toe with madara. of course good old fashioned training and practice is necessary but is zetsu even motivated to do that? zetsu seems to be lacking too many factors that define a shinobi especially a complete will of its own. black zetsu was but a fraction of madara's resigned will and the whites, now seemingly goofy because hashirama was goofy (illustrated past 2 chapters) ..while inheriting some signature hashirama petsonality traits, they dont have all of his personality, ideals, or anything that drives a person to become powerful. they seem to be more like tools of shinobi, ala jutsu, and not shinobi themselves. it was obito's determination and constant training that allowed him to increase mokuton ability, making zetsu a conduit of sorts. the actual hashirama splicing seems different as it behaves as a symbiotic component reflective of hashirama during a certain state of his power (sloppy reasoning) whereas zetsu is not symbiotic but instead more of a true integration. maybe symbiotic is incorrect term but orochimaru/kabuto splices are not true integrations like madara/tobi's gedou bloomed clones.
After the transplant, Sasuke can still use Amaterasu separately, but it seems that he no longer can use Kagetsuchi without Susanoo, since Itachi himself didn't have that jutsu. This might mean, that after transplanting and overriding the eyes (for Uchiha bros), you loose jutsu that weren't compatible, or rather the same as from the person you took the eyes. This might be the reason why transplanting MS and turning it into EMS, rarely worked.
In short, the reason why Madara can only use Susanoo, might be because the other 2 jutsu were not the same as his brothers (so he lost them, although parts of them might have left their imprint on his Susanoo, since the Susanoo does seem to be build upon the previous 2 jutsu). From his Susanoo alone, you can notice that he can't use Amaterasu (which seems to be the source of Susanoo's shield, at least it does seem that way for Sauke and Itachi, seeing as it is the only jutsu that they have sheered beside Susanno). You can notice that Amaterasu form the shield, while their other jutsu, Tsukuyomi and Kagetsuchi, form Susanoo's final weapons (their swords), for Itachi and Sasuke respectively.
I guess this means that the eyes don't combine, but are overridden. The capabilities of the new eyes are limited to what the same jutsu the previous and current user could use. For example, if Izuna's two other jutsu were genjutsu type only, and Madara's ninjutsu, then of course he couldn't use them with Izuna's eyes that are specified for genjutsu and neither could use Izuna's, since Sharingan cannot copy bloodline limits (MS is like a bloodline, within a bloodline limit).
That would also explain why the wood-technique is feared that much. At the very beginning, I thought it's little more than an earth-technique (when it comes to manipulating the ground), and sand seemed even more effective to me than wood. However, if it were known that wood has also chakra-absorbing-capabilities, it would be far more convincing, why it was considered so great.
That makes me wonder whether Kisame was a Senju, too (water-technique as the Tobi-brothers, great chakra-reserves and chakra-absorbing-prowess), but maybe that would stretch it a bit. But, hell, who would have Karin expected to be an Uzumaki. So why not.
^ Well, rather than a Senju for certain, he might have been just one of the So6p's descendants. The Silver and Gold brothers are mentioned just like that, without specifying from which descendant (the younger or the older brother) they came.
Anyway, is it me, or have Tobirama experimented on the Uchiha ? He seems to know way too much, with way too detailed background images and workings of their brains. To even mention that he has seen it countless time, yet strangely enough, no one else knew about it and there was no mention of it, to the point that even Oro didn't seem to know about it. Yep, he might have been, no, he probably was a mad scientist as well. After all, how many people had he sacrificed, before completing Edo Tensei to an usable point/state ?