I think that the biggest challenges in creating a botanical-style aquarium involve the processes- that is, understanding and accepting the processes which occur to get one of these systems "broken in" and thriving. Now, none of the stuff we do is difficult, from a "procedural" standpoint; it's mostly "just prep, place, and wait." The hard parts are deploying patience and making the mental shifts required in the botanical-style aquarium game..
The mental shifts being (for the millionth time, right?) acceptance of a different aesthetic, appreciating biofilms, tannin-stained water, detritus, and organic decay of botanical materials. Understanding that these are the elements of Nature, truly "unfiltered"- and that many (dare I say most?) natural aquatic habitats of the world incorporate several of these elements. Realizing that Nature is not the perfectly arranged, color-coordinated, "golden-ratio"-driven environment that we as aquarists tend to interpret it as.
Back to the process, for a second.
Now, obviously, you're utilizing terrestrial materials in an aquatic environment. Seed pods, stems, leaves, etc. all tend to float initially when wetted. This is part of the reason why we employ a soak/steep/boil for most botanicals. Otherwise, if you just drop 'em in your tank, you'll end up with the botanical equivalent of the Sargasso Sea- a floating "salad" of botanicals topside!
These prep processes help saturate and sink the botanical materials. Some sink more easily and quickly than others. The more durable, "hard-shelled" pods can take an hour or more of boiling just to get them to stay down (I'm thinking about Cariniana Pods and Sterculia Pods here). Their tissues are hard and not the most porous, so the extended soak/boil/steep period is essential if you want them to sink. And of course, as touched on before, this will also release any pollutants bound up in the surface tissues of these botanicals.
Once the botanicals are no longer buoyant, they easily sink to the bottom of your aquarium. And of course, they will begin releasing tannins, humid substances, lignin, and other organic compounds that are present in their tissues. The tannins and humic substances which we covet are just a small part of what is rebased into the aquatic environment, and when you're adding a bunch of material to the aquarium, it's important to observe water quality. We always tell you to go slowly for this very reason- particularly in an established aquarium. These are "dynamic" materials.
After several days or a week, you will see the materials appear to "soften up" just a bit, and perhaps acquire a "patina" of biocover. Most likely, it's in the form of fungal growth and biofilms. These biofilms, in particular, are an incredibly important part of the aquatic ecosystem we aim to replicate in our aquariums, but their appearance is often outside of the aesthetic tastes and expectations of the uninitiated hobbyist!
Your fishes, of course, will have a slightly different opinion...
And of course, the tinted water that seems to accompany our use of botanicals...well, that's a BONUS, in my book!
Yeah, this period is a part of the "game" where we can separate the hobbyists who understand what's really natural from those who have "not done their homework", so to speak. As we've discussed numerous times, biofilms are a completely natural and expected part of utilizing dried botanical materials in an aquarium. The "aesthetics" of this process is not everyone's idea of "beautiful"- and that's understandable.
However, it's a normal, natural, part of the game.
Biofilms will always be present to some extent during the lifetime of your botanical-style aquarium. We need to accept this. During the initial phases, you have several options. You can physically scrub the biofilms off of the botanicals as needed (accepting the fact that they will likely reappear), or observe your natural "biological controls" (such as ornamental shrimp, snails, or even Otocinculus catfish) to help with this process.
In fact, many fishes will forage upon biofilms as part of their diet. Although they are efficient, you shouldn't expect the animals to get everything, and you should not stock your tank with "scavengers" for the sole purpose of eliminating these growths. You can assist with the removal of any offensive materials or...wait it out.
The realization that it's perfectly natural and entirely consistent with the nature of these environments to have some of this stuff present is likely little comfort to you if you just can't handle looking at a field of "yuck" on your botanicals. I can't stress enough the need to make that "mental shift." As we discussed, management of this stuff is entirely up to you and what you can tolerate. Generally, the biofilms, fungal growths, and algae are self-limiting, ultimately disappearing over time as the compounds that fuel them diminish or attain levels that are not sufficient for their growth, or as a result of animals consuming them- or a combination of both.
Ultimately, if you continue to deploy patience and a healthy dose of good old-fashioned aquarium husbandry skill (ie; water exchanges, etc.), your aquarium will fall into a delightful "equilibrium" of sorts- with the botanicals regularly breaking down and transient appearances and disappearances of fungal growths and biofilms during the lifetime of the system.
And of course, that decomposition...the breakdown of botnaicals and leaves is an ongoing process. The decomposition of "transient" materials like leaves and softer pods, etc. is simply part of the natural dynamic, and will continue as long as you choose to employ these materials in your aquascape. If you observe carefully, you may note spawning and other "grazing" behaviors in your fishes, and note that they are spending significant time foraging though the broken-down matter, much like in nature.
Ultimately, the decision to create a "botanical-style aquarium is as much a philosophical one as it is a practical one. To accept nature, rather than to fight it, is a bit at odds with the mindset many of us have with regards to aquarium keeping. As you begin to understand and evaluate your own aquarium, you'll gain a greater appreciation for the wonders of nature, and the processes that have occurred for eons.
Challenge? Perhaps. But the rewards of accepting the challenges could be beyond measure. Rise up to them...
Stay bold. Stay diligent. Stay curious. Stay observant. Stay progressive. Stay enthralled...
And Stay Wet.